Set after the events of The Avengers, Agent Phil Coulson (who survived his apparent death) assembles a small team of agents to investigate a superhuman, Mike Peterson (J. August Richards), who is able to survive an exploding building and a hacktivist group called the Rising Tide that seems to have information. Skye, a member of the Rising Tide, meets with Peterson to warn him about S.H.I.E.L.D., saying that they cover up superhero-based events and that she can help him, which he declines. Later, Skye is abducted by Coulson and Ward and questioned on their plane. She does not cooperate initially, but eventually reveals what she knows. It is later revealed that Peterson had been supplied with the Centipede serum (which is made up of alien metal, gamma radiation, the Extremis virus, and a super-soldier serum) giving him his powers, by an unknown organization that is behind Project Centipede. After visiting the explosion scene, Coulson's team is able to recreate it and learn that it was caused by another subject exploding due to Extremis. While attempting to get info to the team, Skye is kidnapped by Peterson (who is now on the run) and makes her give him a clean slate. Coulson's team is able to track them down and subdue Peterson without him causing mass damage while stopping an assassin that was sent by Dr. Debbie (Shannon Lucio). With Peterson in S.H.I.E.L.D. custody, Coulson offers Skye a place on the team.

Skye is now integrated into Coulson's team as a consultant. Their next assignment is in Peru, tracking an "0-8-4", a S.H.I.E.L.D. code for "an object of unknown origin". Once there, the team quickly realizes that the object is actually a piece of forgotten Hydra technology powered by Tesseract energy. Coulson meets with a former colleague, Camilla Reyes (Leonor Varela), and brings her team aboard the plane. Later, Reyes betrays Coulson and plans to take the Hydra weapon for herself so she can destroy Peruvian rebels. The squabbling team members band together, utilizing each of their talents, and take out Reyes's men. Reyes is taken into custody and Skye texts another member of the Rising Tide, confirming that she has infiltrated Coulson's team. Director Nick Fury (Samuel L. Jackson) scolds Coulson for the damage to the plane and reminds him about the risk Skye poses.

S.H.I.E.L.D. searches for one of its assets, Dr. Franklin Hall (Ian Hart), who was kidnapped by his former research partner, mining philanthropist, and CEO of Quinn Worldwide named Ian Quinn (David Conrad) when his soldiers use a gravity-based weapon on the S.H.I.E.L.D. convoy that was transporting him. He wants to use Hall to take control over the planet's gravity by building a giant "gravitonium" generator. Heading to Malta with the team, Skye volunteers to infiltrate Quinn's mansion during his party so that Coulson and Ward can rescue Hall. Skye tricks Quinn into believing she is betraying S.H.I.E.L.D. for the Rising Tide to get his guard down. However, Coulson soon discovers that Hall perpetrated his own escape and wants to destroy the massive device. Hall believes he is in the right, but Coulson warns him doing so would end up killing millions. Their violent disagreement leads to Coulson being forced not to save Hall as he falls into the middle of the generator, seemingly vaporizing him. Coulson orders that the gravitonium be placed under high security and off the books, however, S.H.I.E.L.D. does not notice that Hall is still somehow alive but trapped within the gravitonium.

There have been a series of thefts throughout the world that are almost impossibly premeditated. Coulson and his team investigates and he uncovers the identity of the thief: his former protégé Akela Amadour (Pascale Armand). Coulson had presumed her dead and does not believe she is capable of turning on S.H.I.E.L.D. despite May's argument that she is nothing more than a weapon. The team nearly catches up to her, but she manages to evade them. When May takes matters into her own hands upon finding her hotel room and Coulson catches up to her, they soon find out she is being blackmailed through a camera (with X-ray backscatter functions) that has replaced her right eye which also has a fail-safe bomb in case she rebels. Coulson takes her to the Bus and hijacks her feed so Ward can take over her new mission. Fitz takes out the bomb while the others work to remove the camera from Akela's right eye. Coulson catches up to who he thinks is the mastermind behind Akela's thefts, but the man is quickly killed through a similar device to Akela's. Coulson and Ward are then left wondering who was actually behind Akela's thefts. Now wearing an eyepatch, Akela is taken away by S.H.I.E.L.D. officers though Coulson promises her she will have a fair trial. Before she goes, Akela tells May something seems different about Coulson. Afterwards, Fitz is playing poker with Ward and taunts him as they play. Ward is unaware that Skye is about to use the glasses he used to simulate Akela's vision to help Fitz cheat, but Fitz changes his mind when Skye tells Fitz she will see him without clothes, and he leaves. She turns them on anyway to check out Ward.

Chan Ho Yin (Louis Ozawa Changchien) is a Hong Kong street magician who dreams of becoming something more. He reveals his secret pyrokinetic ability to a "girl in a flower dress" named Raina (Ruth Negga) who kidnaps him and then promises him fame in exchange for running a few tests on his powers. Upon being informed of Chan's abduction by his handler, S.H.I.E.L.D. Agent Quan Chen (Tzi Ma), the S.H.I.E.L.D. team attempts to trace his whereabouts. They find that it was the Rising Tide who leaked the information that led to his capture and the blame falls to Skye. She protests her innocence and believes she knows another hacker who could have released the info. They head to Austin, Texas where it is revealed that Skye has a relationship with said hacker Miles Lydon (Austin Nichols). After Skye spends the night with Miles trying to learn what she can, Coulson's team arrives. They are both led back to the Bus in handcuffs while the team flies to Hong Kong to rescue Chan. Chan discovers his captors, who are associated with Project Centipede, are injecting him with Extremis which increases the strength of his flame powers. Chan takes on the name Scorch. Back at the Bus, Miles told Coulson that he thought Project Centipede was an environmental activist group. Raina turns on Chan and orders Dr. Debbie (who previously worked on Mike Peterson) and the other doctors to have his blood platelets to be harvested for further experimentation by Project Centipede. Upon being freed during a S.H.I.E.L.D. raid on the Project Centipede facility, Scorch kills Agent Quan, attacks Coulson and May, and incinerates Dr. Debbie while Raina escapes. They are forced to activate the unstable element of Extremis to kill him. Miles is released from S.H.I.E.L.D.'s custody though he is fitted with a tracking device that logs his computer activity as part of his probation. Coulson is told by Ward that Skye hacked the mainframe for them and are unsure if they will find the masterminds behind Project Centipede. Skye is later harshly questioned by Coulson and tearfully reveals that the reason she is with the team and worked for Rising Tide is to find her missing parents, who were connected to S.H.I.E.L.D. in some way. Coulson pledges to help her, but fits her with the same tracking bracelet that Miles was given. Raina visits Edison Po in prison to discuss the outcome of the experiment and asks him to contact the "Clairvoyant".

At the start of the episode Agent Coulson is taking his physical exam. In the lab Agent Ward is testing out a new weapon and says its an ounce too heavy. Once Ward leaves, Skye, Fitz and Simmons are making fun of him by doing impressions of him. Then Agent Coulson and the team investigate a series of deaths involving levitation and electrostatic anomalies. Although the team initially assumed the deaths were caused by some form of weapon, the cause of the anomalies is discovered to be an alien virus found on a Chitauri helmet salvaged from the Battle of New York that turns the unwitting victims into electrostatic bombs. When Agent Simmons is infected by the fatal virus, she and Agent Fitz work feverishly on a cure, while Coulson ignores a direct order from Agent Blake (Titus Welliver) to sacrifice Simmons to save the rest of the team. With time running out and unaware their last attempt was actually successful, Simmons knocks out Fitz to leap from the plane, but Ward manages to save her before she plunges to her death. Simmons and Ward then receives a telling off from Agent Coulson who mentioned how tough it was for him to get the Moroccans to help get them out of the ocean. Once outside his office, Ward mimics Skye, Fitz, and Simmons's impressions of him that he overheard. After his physical reveals nothing unusual, Coulson confides in Agent May he is searching for some explanation for why he feels different. She points out that it would be impossible not to be changed by his seeming death; alluding to having gone through her own life-shattering incident. The helmet is delivered to the S.H.I.E.L.D. Sandbox facility to the possession of Agent Blake, who warns Coulson of the consequences of disobeying a direct order from headquarters.

Coulson and his team arrive at a base called the S.H.I.E.L.D. Hub and are given an assignment by its director Agent Victoria Hand (Saffron Burrows). The assignment calls for Ward and Fitz to head to South Ossetia and disable a weapon device called "the Overkill". Skye and Simmons try to find out more information about the mission, since they are not privy to details about the mission which has been classified as Level 8. Simmons manages to tranquilize Agent Jasper Sitwell who catches her in the act of hacking into top secret Level 8 files. Skye deduces from the information that there is no extraction team coming to pick up Ward and Fitz and Coulson learns about this upon catching her. After a talk with Victoria Hand, Coulson and the team proceed to rescue Ward and Fitz (who manage to disable the Overkill device) as S.H.I.E.L.D. Agents move in on the compound. Coulson did find out that the person who brought Skye to the orphanage when she was young was an as-yet-unidentified S.H.I.E.L.D. Agent. However, Coulson does not tell her the full truth about the file and asks May to discreetly investigate the matter further. Coulson (wanting to find out about his recuperation in Tahiti) is denied access to the information despite his Level 8 S.H.I.E.L.D. clearance. When the person he calls up about it asks if he would like to get approval from Nick Fury about it, Coulson declines and hangs up.

The team assists in the clean-up in the aftermath of the events of Thor: The Dark World and look into a plot to find and assemble three parts of an Asgardian Berserker Staff which imbues the holder with super strength and an uncontrollable rage. They are opposed by a paganist hate group in Norway led by Jakob Nystrom (Michael Graziadei) and Petra Larsen (Erin Way). Phil Coulson tells his team that he has called Nick Fury about it and has been informed that Thor is currently off the grid. Coulson's team is assisted by a professor in Spain named Dr. Elliot Randolph (Peter MacNicol). Touching the staff, Ward relives a traumatic childhood memory involving his abusive brother and a well. He becomes irritable and aggressive and possesses increased strength. Following the clues to the staff parts, the team discovers that Randolph is actually an Asgardian who has lived on Earth for centuries. The team recovers the Asgardian artifact in a battle with the paganist hate group. The staff repairs itself and as Ward and May defeat the paganist hate group. Randolph is convinced to relocate to Portland where Coulson offers to introduce him to Thor when next he is in town. In a hotel, Agent Ward declines Skye's invitation to having a chat in her room and follows Agent May into her room instead. Afterwards, Coulson has a nightmare about his recuperation in Tahiti.

A mysterious force threatens Coulson's team when they bring in a StatiCorp safety inspector named Hannah Hutchins (Laura Seay) who is blamed for an explosion that killed some technicians at StatiCorp's Particle Acceleration Complex where it is believed that she has manifested telekinesis by Coulson. Fitz and Simmons plan a S.H.I.E.L.D. Academy-style prank on Skye revolving around May's past. After the plane makes an emergency landing, they soon discover that the mysterious force is actually a Particle Acceleration Complex worker named Tobias Ford (Robert Baker) who is trapped between Earth and "Hell" (which Tobias believes that he is being dragged to) following the explosion and is targeting Hannah to protect her from those who would try to harm her as he accidentally caused the explosion to get time with Hannah. After Tobias defeats Ward, May manages to defeat Tobias at a nearby barn and convinces him to let go causing Tobias to disappear to an unknown location. Skye is thanked by Coulson for identifying Tobias Ford and getting to know more about May's past. Coulson's team plays a game of Upwords as Fitz comes in with shaving cream on his face, unaware that May was the one who pulled that prank.

Coulson recruits Mike Peterson to his team for super-soldier support when soldiers working for Project Centipede spring Edison Po (Cullen Douglas) from prison following their perfection of the Centipede serum. Coulson's team traces a Centipede-powered soldier named Brian Hayward to an abandoned factory, and walk into an ambush by a squad of Centipede-powered soldiers. When Edison and Raina see that Peterson still has his powers despite not having had an injection in some time, they realize he is the key to Stage 3 of their plan. Coulson's team discover that the soldiers were subjected to the same eye procedure to which Akela Amadour was subjected. Edison tells Raina that he told the Clairvoyant about her and that the last person who tried to find out who the Clairvoyant was stabbed to death. Meanwhile, as Skye investigates the mystery of her parents, Coulson and May are shown to be hiding information from her. When Peterson contacts his son, Ace, he learns that he has been kidnapped by Project Centipede, who wants Peterson in exchange for Ace's safety. When Coulson escorts Peterson to an arranged prisoner exchange, Peterson reveals that Centipede wants Coulson in exchange for Ace, not Peterson, but Peterson cannot go through with this betrayal. Nonetheless, Coulson, to save Ace's life, agrees to be taken prisoner. After the exchange, Peterson tries to rescue Coulson, but Centipede sets off an explosion, in which Peterson is presumed killed. After Raina escapes with Coulson, she tells him that he only needs to give Project Centipede the information regarding how he came back to life the day after he died.

Victoria Hand is assigned to lead S.H.I.E.L.D.'s efforts to rescue Coulson while his captors Project Centipede torture him to learn the secret of his resurrection. Believing Skye to be untrustworthy, and after seeking May's input, Hand has Skye removed from the Bus. S.H.I.E.L.D. captures Mr. Vanchat, a black market dealer and an associate of Raina's. Ward manages to get Mr. Vanchat to supply S.H.I.E.L.D. with information on her. Skye sets out on her own investigation. She impersonates May and coerces Lloyd Rathman, a businessman of questionable dealings, to assist her into hacking into secure files. Coulson is initially tortured by Po, who tells him that the Clairvoyant cannot glean the information they want because the Clairvoyant has been unable to sense Coulson since his resurrection. The Clairvoyant decides that Po's methods are ineffective and kills him, after which Raina takes over Coulson's interrogation. She uses a scanning device to compel him to remember aspects of his being brought back to life. Coulson experiences flashbacks in which a reluctant Dr. Streiten (Ron Glass) and others operated on him. During these flashbacks, Coulson's skull cap was removed and his brain was being directly stimulated by a robotic apparatus, while Coulson begged to be allowed to die. After S.H.I.E.L.D. rescues Coulson, he confronts Streiten, who tells Coulson he had been dead days, not minutes, and was resurrected at the orders of Director Fury. Streiten reveals that after his revival, Coulson had lost the will to live, and that the doctors manipulated Coulson's brain to give him false memories and restore his will to live. It is later revealed that Peterson is alive, albeit badly burned, missing the lower half of his right leg, and has had an explosive surveillance eye implanted in him by someone working for the Clairvoyant.

While at a S.H.I.E.L.D. Academy, Ward, Fitz, Simmons, and Skye investigate an attack upon students which was perpetrated with an "ice machine", a device that can freeze people and their surroundings. During their time there, another ice machine goes off freezing cadet Donnie Gill (Dylan Minnette), though the agents are able to save him. While the rest of the team are interrogating the other cadets, Fitz gets to know Donnie, seeing much of himself in him and helping him solve a problem with a new power source Donnie has invented. The team learns that Donnie and his fellow cadet Seth Dormer (Daniel Zovatto) are behind the ice machines and that the power source Fitz helped him perfect was for a larger version of it. Meanwhile, Coulson and May head to Mexico City to find a former agent named Richard Lumley (Boyd Kestner), who tells them of a mission 24 years earlier involving an 0-8-4, which turned out to be Skye. He warns them that she is dangerous, as many agents, including his partner, Linda Avery, died trying to protect her. After meeting with the rest of the team, Coulson relates what Lumley revealed to Skye, who is devastated at the revelation. Donnie and Seth activate the larger device, causing a huge ice storm that Seth hopes will impress Ian Quinn, for whom Seth's father works as a lawyer at Quinn Worldwide. Realizing his mistake, Donnie attempts to shut it down, but a bolt of lightning destroys the machine and puts Seth in cardiac arrest. May tells Coulson about her sexual relationship with Ward; Coulson says he trusts her to comport herself responsibly, but adds that, if it becomes a problem...to which she responds she will break it off. The team apprehends Donnie but is unable to save Seth's life. On his way to the Sandbox for observation, Donnie realizes that the explosion of the ice machine has given him cryogenic abilities. Ian Quinn receives a call from Coulson warning him that if his aircraft flies over any country that is a S.H.I.E.L.D. ally, it will be shot down. Before hanging up, Quinn gives Coulson a message that the Clairvoyant says "hello".

In order to find the Clairvoyant, the team boards a train in Italy on which a Cybertek Inc. security group led by Carlo Mancini (TJ Ramini) is shipping a package to Ian Quinn. They take over the mission for an Italian police member named Luca Russo (Carlo Rota). The team splits into groups, with Coulson and Simmons posing as a father and daughter while Fitz and Skye work with Ward and May to track down the package. However, the group is exposed, leaving Coulson and Ward to flee the train. May also goes missing, but when Coulson and Ward track her down, they learn the team was sold out by Luca Russo, who is killed by May. The team finds the train and Simmons, but Fitz and Skye are gone, having disembarked to track the package to Quinn's mansion. In the basement, Skye is confronted by Quinn and Mancini, who reveal that Mike Peterson is alive, having been kept in a hyperbaric chamber. Mancini opens the package containing a high-tech prosthetic leg that he fits onto Peterson's amputated right leg. To test Peterson's obedience to Project Centipede, Quinn orders him to kill Skye. He refuses, stating that Skye is not who the Clairvoyant wants him to kill. Instead, Quinn then shoots Skye twice in the stomach and leaves her for dead stating that he has his own orders. Peterson then executes the Cybertek security team because they led S.H.I.E.L.D. to the mansion. Quinn walks right into a S.H.I.E.L.D. raid on the mansion. Quinn is arrested, but Skye is left near death and Simmons can only sustain her temporarily by placing her into Peterson's hyperbaric chamber. Peterson, who has gained his new prosthetic leg through "Project Deathlok", secretly observes his son at a playground and requests the Clairvoyant to let him see his son by writing on a piece of paper for the Clairvoyant to read. The Clairvoyant says "not yet".

Skye is rushed to a S.H.I.E.L.D. medical facility to save her life. The doctors are only able to stabilize her, forcing Coulson to bring her to the S.H.I.E.L.D. location where he was revived. Agents John Garrett (Bill Paxton) and Antoine Triplett (B.J. Britt) board the Bus in order to claim Ian Quinn, who Garrett's men had been pursuing, and bring him to the Fridge for questioning, as Coulson refuses to turn him over. Garrett compromises with Coulson when he realizes he is keeping Quinn until he can save Skye. Through interrogating Quinn, Coulson, and Garrett learn that the Clairvoyant made Quinn shoot Skye, so he could learn how Coulson came back from the dead. Fitz and Simmons, who are looking over Coulson's medical files, realize that S.H.I.E.L.D. did not revive Coulson, rather a place known as the "Guest House". They realize a specific drug would be there to help Skye. At the "Guest House", Coulson, Ward, Garrett, and Fitz enter and find the place rigged with explosives after taking out the only guards. Fitz is able to find the drug, while Coulson finds a room marked "T.A.H.I.T.I." Fitz races back to the Bus to deliver the drug while Coulson explores the room. Inside, Coulson finds more of the drug as well as discovering that the drug is coming from the upper half of a blue-skinned humanoid corpse. Everyone is able to get out before the facility implodes. Coulson races to prevent Fitz giving Skye the drug, based on what he saw in the T.A.H.I.T.I. room. Fitz gets the drug to Simmons in time to save Skye. Lorelei (Elena Satine) arrives at a motel in Death Valley and comes across a newlywed couple. She mesmerizes the man, who drives away with her, leaving his wife at the motel.

Lorelei ditches her previous victim for a biker whose gang she enslaves for her plans to create an army. While talking to Skye, who has finally awoken from her coma, the team is summoned by May to investigate an energy reading in the desert consistent with the imminent arrival of an Asgardian. They encounter Lady Sif (Jaimie Alexander), who has come to Earth seeking Lorelei. Reuniting with Coulson, Sif explains that Lorelei escaped imprisonment in Asgard during the attack of the Dark Elves and that to neutralize her power to control the minds of men, Sif must fit a special collar around Lorelei's neck that prevents her from speaking. The team and Sif travel to the biker bar Lorelei is using as a hideout, but during the battle, Lorelei enchants Ward and escapes with him. They go to Las Vegas, where Lorelei and Ward have sex in a hotel room, but when Coulson, Sif, and a S.H.I.E.L.D. team catch up, the two are nowhere to be found. They realize too late that Ward and Lorelei, planning to eliminate any threats to Lorelei's rule, have commandeered the Bus with help from an enchanted Fitz, who locks Sif in the interrogation room and imprisons Simmons in Skye's recovery room. Coulson, pretending to be under Lorelei's power as well, learns of Simmons's location and frees her. Lorelei encounters May and claims that Ward revealed to her that despite their sexual relationship, his heart is with someone other than May. Simmons and Skye help trick Lorelei into entering the interrogation room, where Sif confronts her; while they fight, May is forced to do battle with Ward. Sif finally manages to disarm Lorelei, and despite Lorelei's attempts to get Sif to kill her, Sif fixes the collar to Lorelei's neck, undoing her enchantment on Ward and Fitz. Sif thanks Coulson for the team's aid and says that she will bring Lorelei back to Asgard on Odin's orders, and let Coulson be the one to tell Thor he is not dead. May ends her relationship with Ward. Coulson goes to Skye and confesses that he discovered the drug used to revive them both was alien in origin based on his own suspicions and information provided by Sif. Despite how disturbed Coulson is by this fact, Skye remains optimistic, and Coulson swears that they will get answers, beginning by tracking down the Clairvoyant once and for all. He orders Skye to keep the origin of the drug a secret until Nick Fury gives them the truth. It is revealed that May is secretly monitoring Coulson when she makes a call and tells the party on the other end that "Coulson knows".

Garrett and Triplett are attacked by Mike Peterson, who has been reborn as Deathlok, at a S.H.I.E.L.D. safehouse. Several weeks later, they along with Agents Hand, Sitwell, and Blake join the team in their hunt for the Clairvoyant. The agents split into teams to pursue leads on different Clairvoyant candidates. At a nursing home searching for Thomas Nash, a catatonic man who once claimed to be a psychic, May and Blake encounter Deathlok. Before critically injuring Blake and escaping, he claims that "Mike Peterson is dead" upon being reminded of his son. However, Blake manages to tag him with a tracker before he flees. Concluding that Nash is the Clairvoyant because of Deathlok's presence along with the falsification of his nursing home records, the team converges on Deathlok's next location, an abandoned horse racing track while Triplett and Simmons stay behind at the Hub with Hand. The team briefly encounters Deathlok again, but he flees into the sewers. However, they discover a hidden room where Thomas Nash (Brad Dourif), a vegetative man on life support who must speak through a computer, is hiding. Nash surrenders and boasts that as the Clairvoyant, he will always be watching them. But when he says that Project Centipede will kill Skye, Ward shoots him dead. Meanwhile, Fitz attempts to create a secret phone line so he can speak to Simmons from the Bus, but he discovers a bug that leads him to May's secure line. Coulson realizes that Thomas Nash was not the Clairvoyant, and when Skye presents the results of her studies on the S.H.I.E.L.D. psychological files of the potential Clairvoyants, they realize that the Clairvoyant is a member of S.H.I.E.L.D. with access to the same files, giving the Clairvoyant knowledge of how to manipulate the agents. Coulson accuses the detained Ward of working with the Clairvoyant and shooting Nash to misdirect away from the Clairvoyant's true identity, but they are interrupted by Skye, who learned of May's unapproved phone line from Fitz. Coulson and Skye end up in a standoff with May in the Bus's hangar. But as May tries to explain that she cannot identify who the line goes to, control of the Bus is hijacked. At the Hub, Victoria Hand orders everyone aboard to be killed except for Coulson.

Garrett's jet is attacked by S.H.I.E.L.D. drones after the Bus is hijacked, and he rejoins the team. At the Hub, Simmons and Triplett begin working together to secretly upload Simmons's research on Skye's blood, only for a Hydra assault on all S.H.I.E.L.D. facilities forces them into hiding. Coulson locks May up in the interrogation room with Ward, still believing she is the traitor. Skye discovers a secret code in a signal on S.H.I.E.L.D.'s network that she deciphers to reveal Hydra's infiltration. When the Bus arrives at the Hub, the group splits into teams to capture Victoria Hand, whom they believe is the Clairvoyant. However, Hand reveals that she is not a member of Hydra but believes that Coulson is, and recruits Triplett and Simmons to aid her in stopping Hydra. Garrett accidentally discloses information that unwittingly reveals himself as the true Clairvoyant, and is captured by Coulson and May. Ward volunteers to accompany Hand to the Fridge so he can see to Garrett's imprisonment personally. However in transit, Hand offers Ward the chance to execute Garrett to atone for killing Thomas Nash by mistake. Instead, Ward kills Hand and her agents, freeing Garrett and revealing his own allegiance to Hydra.

Ward frees Raina and introduces Garrett to her as the Clairvoyant. Despite her initial disappointment that Garrett does not actually have any psychic powers, he tasks her with conducting research on the Guest House drugs for Project Centipede, which was secretly backed by Hydra. Meanwhile, Colonel Glenn Talbot (Adrian Pasdar) contacts Coulson and informs him that a military team is en route to the Hub. Not trusting Talbot, Coulson leaves with the team and Triplett. He orders Skye to erase the identities of all the team members, including Ward. However, when Coulson collects the team's badges, he discovers a hidden message with coordinates in the Canadian wilderness. There they discover the hidden S.H.I.E.L.D. base, Providence, run by Agent Eric Koenig (Patton Oswalt). Coulson learns from Koenig that Fury is alive but is told to keep the information secret. He also learns from May that Fury did not oversee the T.A.H.I.T.I. project. Elsewhere, Ward and Garrett infiltrate the Fridge, freeing its prisoners and stealing weapons including the Berserker Staff and the 0-8-4 from Peru. At the Hydra base, Raina informs Garrett that the hard drive containing all of Skye and Simmons's research is specially locked with a password only Skye holds, prompting Garrett to send Ward to Providence to obtain it. Later, Ian Quinn is brought to the Hydra base. Though angry at Garrett for his imprisonment, his ire is softened when Garrett shows him that he has Quinn's gravitonium which was retrieved from the Fridge.

Koenig subjects Coulson's team to a rigorous lie detector test, which Ward narrowly beats to maintain his cover. Afterwards, Coulson takes Fitz, Simmons, and Triplett to stop Marcus Daniels (Patrick Brennan), a superhuman possessing the Darkforce and former Fridge inmate who is obsessed with cellist Audrey Nathan (Amy Acker), Coulson's former love interest. After rescuing Audrey, they devise a plan to lure out Daniels. The group overload him with energy, causing him to explode, and incidentally knocking out Audrey. Coulson briefly comforts her before withdrawing, as he plans on telling her he is alive someday. Meanwhile, May leaves the team after repairing the Bus, tired of Coulson not trusting her. Skye and Koenig hack the NSA to get eyes on the Hydra attack at the Fridge, forcing Ward to murder Koenig to prevent discovery and he tries to seduce Skye. Skye finds Koenig's body and realizes that Ward is with Hydra. In order to avoid suspicion by Ward, Skye joins him as they steal the Bus before Coulson and the others return to Providence. Later, May is picked up by her mother (Tsai Chin) in Ontario, Canada and is revealed to be searching for Maria Hill.

While May meets with Hill in Washington, D.C., Coulson's team discovers that May, Ward, and Skye left Providence. Simmons discovers Koenig's dead body while Fitz finds a message left by Skye informing them that Ward is a member of Hydra. Hill leads Talbot's team to Providence, though Coulson later convinces Hill to help him and his team escape. Skye leads Ward to the diner where she met Mike Peterson and secretly tips off the police. She reveals that she knows his secret and escapes while he fights the police, but is captured by Deathlok. When Skye refuses to decrypt the hard drive, Deathlok forces her compliance by threatening to kill Ward. As Ward tries to fly the Bus away, he is confronted by Hill and Triplett, who stall long enough for Coulson to sneak on board through the landing gear. Coulson frees Skye and they escape in Coulson's flight-capable car, Lola. Deathlok attempts to convince Ward to let them go now that the drive is in the process of being decrypted, but Ward refuses. The team retreats to a hotel where Skye reveals she left a trap in the hard drive. May returns and shows Coulson the contents of a flash drive she recovered from his false grave. The file is a video of Coulson himself, who is revealed as the director of T.A.H.I.T.I., informing Fury that the project must be shut down because of horrific side effects the drugs had on test subjects, which could only be mitigated by erasing the victim's memory of what happened.

In a series of flashbacks, a teenage Ward is seen meeting Garrett at a juvenile detention facility, where he is being held after trying to burn down his family's home. After agreeing to join the secret organization Garrett says he works for, Ward is left in the wilderness alone, forced to survive for months until Garrett returns. Garrett eventually tells him about Hydra's presence within S.H.I.E.L.D., and Ward agrees to join. In the present, the team connects Project Centipede, Garrett, and others to a common source: Cybertek. Coulson and May infiltrate Cybertek to activate Skye's trojan she left on the hard drive, only to find file cabinets instead of mainframes. However, they learn that Garrett was the first subject for "Project Deathlok", which began in 1990. As such, Garrett's implants are failing. With a few months to live, he is desperate to complete the Project Centipede serum in order to save himself. Coulson's team finds the Hydra base in Cuba, but Garrett's men have already left, with the exception of several Centipede soldiers. Ward captures Fitz and Simmons, who had split from the others to find the Bus, but Fitz is able to use an EMP device to short out Garrett's body. The dying Garrett orders Ward to kill Fitz and Simmons, who hide from him in a locked room. Ward struggles with following through on the orders, deciding to eject the room into the ocean. Raina injects Garrett with the synthesized Guest House drug to work with his Project Centipede serum. Initially, the drug seems to cause an Extremis reaction, before Garrett stabilizes and claims to "feel the universe". In Washington, D.C., Ian Quinn proposes the sale of Deathlok soldiers to the US government, using Mike Peterson's assassination of a Colombian drug lord as evidence of the program's success.

At Cybertek, Quinn begins his presentation to U.S. military officials only for Garrett to interrupt and kill one of the generals. Evading the Centipede soldiers, Coulson and his team raid the Cybertek facility, with Skye saving Mike Peterson's son, May fighting Ward, and Coulson confronting Garrett. Elsewhere, Nick Fury rescues Fitz and Simmons though Fitz is barely alive. Coulson engages Garrett but is overwhelmed until Fury arrives for support. Coulson and Fury push Garrett back, with Deathlok delivering a finishing blow once he learns Skye has saved his son. In the aftermath, Ward and the Centipede soldiers are arrested. Mike Peterson, unable to face his son, goes off on his own to redeem himself. Garrett attempts to utilize the newest Deathlok armour, only to be vaporized by Coulson. Afterwards, Fury explains his respect for Coulson and appoints him as the new Director of S.H.I.E.L.D., leading his team to a secret base run by Billy Koenig. Raina delivers a photo of Skye to a mysterious, blood-soaked man, telling him she found his daughter, Skye. Later, Coulson awakens in the middle of the night and begins exhibiting signs of the same enhanced mental capacities and fixation that Garrett experienced.

In 1945, Agent Peggy Carter and the S.S.R. raid the last known Hydra base (led by Werner Reinhardt) and confiscate many items, including the Obelisk and a blue body. In the present, Phil Coulson's team monitors a deal revolving around the Obelisk, which goes awry when Carl Creel kills the ex-S.H.I.E.L.D. agent offering the intel and escapes with it. Agent Skye interrogates Grant Ward and learns that Hydra is using communication channels not monitored by S.H.I.E.L.D. The team realizes that General Glenn Talbot is in trouble and rushes to rescue him from Creel, before abducting Talbot themselves and using him to break into a military facility full of confiscated S.H.I.E.L.D. assets. Agent Isabelle Hartley finds the Obelisk, while Skye and Agent Antoine Triplett steal a cloak-capable quinjet. Lance Hunter leaves with his team of mercenaries enlisted by S.H.I.E.L.D., only to be ambushed by Creel, whose attack kills Hartley. Creel then steals the Obelisk for an apparently un-aged Reinhardt, now going by the name Daniel Whitehall.

Following Creel's theft of the Obelisk, Hunter is captured by Talbot's men. Creel absorbs the properties of the Obelisk and accidentally kills a waitress in a bar. He later meets Raina, but declines her offer to help him. Talbot tries to persuade Hunter to work for him and sets him free, but Hunter returns to S.H.I.E.L.D. wanting revenge for his fallen friends. Agent Leo Fitz and the mechanic Agent Mack are able to build a weapon that can incapacitate Creel. As the team observes Creel making a deal with Whitehall's second-in-command Sunil Bakshi, Hunter disarms the other agents and tries to kill Creel himself. However, Creel easily defeats him. Just as he is about to kill Hunter, Coulson incapacitates Creel with the new weapon. Coulson later asks Hunter to stay and help S.H.I.E.L.D., and then tells Talbot that he is wasting his time tracking S.H.I.E.L.D. and turns Creel over to him. The Obelisk is later shown in the possession of Raina and Skye's father - "The Doctor" - who is asking the former to find his daughter.

Coulson learns from Agent Jemma Simmons, who is working undercover within Hydra, that their next planned target for recruitment is Donnie Gill, and Ward explains to Skye that Hydra brainwashes promising recruits such as Creel. S.H.I.E.L.D. traces Gill to a Hydra ship in Morocco, while Hydra sends Simmons with a team to find Gill themselves, as a test of her loyalty. Fitz reveals to Ward that Gill is the target, and Ward warns that Gill was a Hydra asset already, and that Hydra would try to reactivate his brainwashing. Agent Melinda May, who knows of Simmons' mission, allows her and Gill to escape, to maintain Simmons' cover, and Hydra successfully re-brainwashes Gill. Skye manages to shoot him, and he falls into the water and freezes, but government forces are later unable to locate his body. Whitehall decides to promote Simmons, despite her failure to retrieve Gill, and Ward tells Skye that her father is alive and offers to bring her to him.

Coulson and May go undercover to a charity function to get a painting that is carved with alien symbols, and encounter Talbot, who has already claimed it, and asks to meet with Coulson in private. Coulson sends May to scout ahead, and she discovers the brainwashed S.H.I.E.L.D. Agent 33 in Talbot's hotel room, realizing that the Talbot at the party was actually Bakshi in disguise. Bakshi tortures May while Agent 33 disguises herself as May to pick up Coulson and sabotage the Bus. Coulson realizes that "May" is a fake because of inconsistencies in her behavior. He rescues the real May, who defeats Agent 33, while Fitz and Hunter work together to save the Bus from Hydra's computer virus, allowing Fitz to start reintegrating into the team following previous life-changing injuries. Though Bakshi escapes, S.H.I.E.L.D. claims the painting, hiding its survival from the real Talbot. Raina is later confronted by Whitehall, who orders her to deliver the Obelisk to Hydra or face death.

Raina begs Skye's father to give her the Obelisk, but he angrily berates her for not delivering Skye, then kills two men who he was performing surgery for. Raina discovers Simmons' cover and attempts to blackmail Coulson: she will not reveal Simmons to Hydra if she can take Skye to her father. Coulson refuses the offer and Simmons' identity is exposed, though Hydra security chief Bobbi Morse, another undercover S.H.I.E.L.D. agent, rescues her. Coulson has Raina tagged so she can lead them to Hydra, and she discloses the location of Skye's father. At his abandoned hideout, the team finds the bodies of the men he murdered, and he realizes, watching through hidden cameras, that Skye thinks he is a monster. Coulson later shows Skye alien symbols he has been compulsively carving, which she believes are a map. Fitz and Simmons are reunited while Morse, who is Hunter's ex-wife, joins the team. Skye's father delivers the Obelisk to Whitehall himself and offers to join forces with Hydra.

During a United Nations meeting on S.H.I.E.L.D., Hydra agents posing as S.H.I.E.L.D. operatives attack and kill several world representatives. Senator Christian Ward, the brother of Grant Ward, decides to use this incident to propose a multinational anti-S.H.I.E.L.D. initiative. As Coulson meets Christian to propose a win-win solution, Skye interrogates Grant about Christian. Grant explains to Skye that Christian is a master manipulator, Christian tells Coulson that this is a lie, with both S.H.I.E.L.D. agents attempting to ascertain which Ward brother is being truthful. Christian and Coulson agree to abandon the anti-S.H.I.E.L.D. proposal in exchange for Grant's transfer to Christian to stand trial, but Grant escapes while being transferred. May leads a team against the Hydra agents who attacked the UN, capturing several agents, and turning them over to Talbot, who begins to agree with Coulson's mission and offers his condolences for fallen S.H.I.E.L.D. agents.

Since being resurrected by S.H.I.E.L.D.'s Project T.A.H.I.T.I. using the experimental drug GH-325 (derived from the alien corpse Carter discovered in Whitehall's possession), Coulson has been compulsively carving the alien symbols. When a former S.H.I.E.L.D. agent and patient of T.A.H.I.T.I. is killed and her body carved with the symbols (by the former agent who had carved the painting previously), Coulson uses Hydra's memory machine to find other patients who were injected with the drug. He goes after the remaining patients, trying to find an end to the madness. He discovers that the writing is actually a 3D diagram of a city where the alien host of GH-325 apparently wished to go. Seeing the completed design ends his need to carve, but since Hydra is also searching for the city, he makes it a priority for S.H.I.E.L.D. to find it first. Meanwhile, the other members of the team try to capture Ward, who betrays Hydra by capturing Bakshi and leaving him for S.H.I.E.L.D., before preparing to meet his brother.

Bakshi accidentally reveals to Morse that Whitehall is actually Reinhardt, a Nazi scientist who was working on the Obelisk before being captured by the S.S.R. and imprisoned for life by Carter in 1945. In 1989, Reinhardt was released from prison by Alexander Pierce, to find that a woman he had found in 1945 was still the same age. Dissecting her, Reinhardt discovered the secret to her immortality, and used it to make himself 44 years younger. "The Doctor" finds the remains of the woman, who was his wife, and vows vengeance against Whitehall, who he is now pretending to be allied with. Grant Ward also appears to join in an alliance with Whitehall, after having tortured Christian into confessing past sins, and then apparently murdering him and their parents. S.H.I.E.L.D. hacks a USAF mapping satellite and use it to find the hidden city, and Coulson meets "The Doctor", who knows that the Obelisk (or the Diviner) is a key that must be taken to the city by someone it deems to be worthy.

The team splits up, with Coulson and Morse leading a group to begin searching for the hidden city under San Juan, and May, Skye, and Hunter leaving to help Agents Sam and Billy Koenig rescue Raina from a Hydra kidnapping attempt in Vancouver. Raina tells Skye that they are two of the "worthy ones" who could enter the temple in the city, and that any others who try will die. She also reveals that the city and Diviner were created by the Kree. Skye tries to warn the main team, but Whitehall blocks their communications, and Ward boards the Bus to take Raina. He also takes Skye, promising to take her to her father, and in exchange agrees to let the others go. Mack has already entered the city, which causes him great pain and compels him to attack the others, until he is subdued by Morse and falls down a deep shaft. Whitehall, surprised to learn that Ward took Skye and did not destroy the Bus as ordered, gives Agent 33 (who still has May's face, but is now disfigured) orders to do so.

May evades Hydra's attempt to shoot down the Bus. Ward brings Skye to meet her father, Cal, who explains that her name is Daisy, and that Whitehall killed her mother. Arriving at the Hydra base in San Juan where they are drilling into the temple, Whitehall immobilizes Cal and menaces Skye, but is interrupted as Coulson's team assaults the base. Coulson kills Whitehall, taking Cal's chance of vengeance, leading the latter to attack Coulson. Skye shoots Ward and forces Cal to leave, before following Raina and the Diviner into the temple. Agent 33 assists Ward in escaping. Coulson and Triplett race to the temple, with Triplett making it in and Coulson being delayed by Mack, who soon after breaks from the city's control when the temple closes itself and the Diviner opens, revealing a large crystal. Skye and Raina are encased in cocoons, while Triplett is killed by the Diviner. Skye erupts out of her cocoon as an earthquake shakes the city. Elsewhere, another Diviner reveals to a man with no eyes that "there's someone new".

In the wake of Triplett's death, Coulson looks to hit back at Hydra, who are considering having Bakshi fill Whitehall's leadership position. S.H.I.E.L.D. enacts a plan that sees Bakshi escaping and leading them to other high-ranking Hydra agents, who are then killed. In San Juan, the alien city is flooded, but not before a transformed Raina escapes, now with a monstrous appearance. When Cal turns his back on her, reminding her that she got what she wanted, Raina attempts to commit suicide, but she is taken by the man with no eyes, Gordon, who can teleport. Fitz and Skye realize that the latter has also been transformed—she caused the earthquake in San Juan, but has no control over this ability. Fitz agrees to keep her secret and hides the truth from the rest of the team. Meanwhile, a model car that Mack built for Coulson scans the latter's office and finds the "toolbox” that previous S.H.I.E.L.D. Director Nick Fury gave to him. Mack, who has been studying the S.H.I.E.L.D. base's schematics, secretly reports this to Morse.

S.H.I.E.L.D. is called in to help an amnesiac Sif, who was last seen fighting an incredibly strong man, and is searching for something called "Kava", which they soon discover is the location where Whitehall had found the Diviner. There they capture the man, who restores Sif's memories and introduces himself as a Kree named Vin-Tak who has come to destroy all the Diviners, and kill anyone affected by the Terrigen crystals inside. When Skye's abilities are revealed, Sif and Vin-Tak attempt to capture and kill her, respectively, but Morse wipes Vin-Tak's memories using his weapon, while Coulson convinces Sif to leave Skye be. Sif returns Vin-Tak to his planet, warning Coulson that the Kree should no longer be a problem, but Skye may be a greater danger than he realizes. Meanwhile, Morse tries to end her rekindled relationship with Hunter when Mack warns her that he is getting too close, but Hunter angrily confronts Mack about this and his suspicions that Mack and Morse are hiding something, forcing Mack to knock him unconscious.

Cal recruits dangerous individuals from S.H.I.E.L.D.'s Gifted Index to settle his vendetta. Coulson and Morse investigate, and are led to the former's hometown of Manitowoc, where the criminals have seized the local school stadium. May enlists Dr. Andrew Garner, her ex-husband and a psychoanalyst, to work with Skye, who is now on the Index herself. During one of Garner's talks with Skye, Coulson requests back-up, prompting May to fly the Bus to Manitowoc, with Garner and Skye on board. At the stadium, Coulson is confronted by Cal, while May arrives, bluffing to kill Skye. During the stand-off, Gordon appears and teleports away with Cal. As Coulson's team subdue Cal's group, Skye starts causing tremors, only stopping this by directing her abilities inward, causing hairline fractures throughout her body. Elsewhere, Mack hides Hunter in a safe house until they are extracted by an organization that Mack calls "the real S.H.I.E.L.D.", and Gordon takes Cal to his superiors, belittling him for using science to increase his strength.

On Garner's recommendation Coulson pulls Skye from active duty, and leaves her at a safe house with gloves designed to help repress her abilities, asking her to take some time to learn to control her powers. Ward and Agent 33 hunt down the man who created the technology that allowed Agent 33 to take on May's appearance. He fixes her mask so she can once more change her appearance to anyone she wishes. Using this, they infiltrate Talbot's base and break out Bakshi, who S.H.I.E.L.D. had handed over as a sign of good faith. From Bakshi they learn about Agent 33's life before he brainwashed her, including her name, Kara Palamas, before brainwashing him themselves. Mack introduces Hunter to Robert Gonzales and the leadership of the "real S.H.I.E.L.D.", founded on the ideal of transparency rather than Fury's mantra of compartmentalization. They see Coulson and his erratic behavior as a threat, and when Hunter escapes they decide to attack Coulson's group immediately.

Gordon visits Skye to tell her of his home, where she can be safe and learn to control her powers without S.H.I.E.L.D.'s gloves. Coulson confronts Mack about the model car and his behavior, deducing that he is a mole. Morse steals the toolbox from Coulson's office and takes over the base's systems, allowing her and Mack to evade capture, and the rest of their faction to attack. This organization was formed when S.H.I.E.L.D. fell and Morse, Gonzales, Mack, and Hartley disobeyed Fury’s orders, saving hundreds of loyal S.H.I.E.L.D. agents. Gonzales realized all the harm caused by Fury and his secrets, and now wants S.H.I.E.L.D. to exist without them. He and his colleagues fear potential alien/superhuman phenomena that could endanger the rest of the world, including Skye, but when they try to detain Skye, she accidentally unleashes her abilities. Horrified at what she can do, Skye agrees to go with Gordon. May helps Coulson escape from Gonzales, and he soon finds Hunter, who agrees to become a permanent agent.

Gordon takes Skye to Afterlife, a haven, where Lincoln explains to her that most people who are transformed are chosen and prepared for it, and then a guide is selected to help these people master their new abilities. Skye's guide is the founder of Afterlife, Jiaying, while Gordon will guide Raina, who still wants to die. When Gonzales asks Fitz and Simmons to help them open Fury's toolbox, Fitz refuses and decides to leave S.H.I.E.L.D., while Simmons agrees to help, though this is a ruse so that Fitz can take the toolbox with him. Coulson and Hunter steal a quinjet from Gonzales' agents with the help of Agent Mike Peterson, who has been hunting Hydra scientist Dr. List, and found him experimenting on gifted people. With the appearance of Peterson, Gonzales fears how many super powered operatives Coulson has, but believes that he still deserves fair representation, and so asks May to serve on their S.H.I.E.L.D. board. Coulson soon realizes that the person most involved in this Hydra threat that they can turn to is Ward.

Now in charge of Coulson's base, May agrees to look into his actions since he became Director, finding that Coulson has been secretly building another base and consulting with Garner, which Mack believes is because he is creating a gifted army. Skye is training with Jiaying, and begins to focus her abilities to manipulate objects' natural frequencies. Jiaying soon reveals that she is Skye's mother—Cal had pieced her back together, her healing factor revived her, and they searched for Skye, who S.H.I.E.L.D. had taken, until Jiaying realized what monsters they had become, and left Cal to build a new and peaceful life. Their relationship must remain a secret because once a member of their group stole Terrigen crystals for her daughter, who then forced her mother to hurt others to feed on their pain. They were stopped when May killed them both, scarring her for life. However, Jiaying and Skye do agree to join Cal for dinner, a moment that Raina apparently foresaw in a dream. Fitz opens the toolbox, and uses it to contact Coulson.

Coulson, Hunter, Fitz, and Peterson capture Ward and Palamas and make a deal to infiltrate Hydra in exchange for giving Ward a clean slate by wiping his memories. Ward uses the brainwashed Bakshi, along with Peterson, to get close to List, and they learn that he has been tracking Gordon and seeks to capture him. Jiaying intends to banish Cal from Afterlife, but Skye fears he may harm innocents, and so goes with him, before calling May for help. Simmons hacks into Peterson's cybernetic eye, and through his video feed S.H.I.E.L.D. discovers that Coulson is working with Ward. May sends Bobbi and Mack. As Cal is enjoying spending time with Skye, they discover that Lincoln is spying on them, and Cal realizes Jiaying's plans. Hydra tracks Gordon's movements to Cal's office, and attack before Cal can do anything about Lincoln. Hydra captures Peterson and Lincoln. Skye is almost reunited with Coulson, but Gordon takes her and Cal away. When Bobbi and Mack arrive, Coulson surrenders to them.

Coulson offers to take his own team to infiltrate List's base and free Peterson and Lincoln. Raina foresees Skye saving Lincoln's life, and they convince Gordon to take her to S.H.I.E.L.D. without telling Jiaying, who allows Cal to stay in Afterlife (though he does accidentally reveal to the community that Skye is their daughter). Coulson, May, Skye, Fitz, Simmons, and Ward infiltrate the Hydra base with the help of Bakshi on the inside. Simmons and Ward save Peterson, but Simmons attempts to kill Ward for all that he has done to them. Bakshi sacrifices himself to save Ward, who decides to leave by himself. Skye does save Lincoln, while Coulson discovers the base of Hydra's leader, Baron Wolfgang von Strucker. He gives the location to Maria Hill so that the Avengers can defeat Hydra. Ward leaves Palamas with S.H.I.E.L.D., hoping that she can reclaim her lost life as an agent, while Raina, who is beginning to question Jiaying's leadership, foresees metal men destroying cities.

The S.H.I.E.L.D. board is grateful to Coulson after Fury uses Coulson's secret helicarrier to help save the world, and they agree to merge their factions, with Coulson remaining as director, and the board acting as his oversight and advisory council. Raina has a vision of an ancient Kree weapon, designed to destroy the Inhumans - those who were altered by the Kree. Gordon takes her to search for it, finding it in the cargo hold of Gonzales' ship. S.H.I.E.L.D. discovers the intruders, and uses Hydra technology to track them when they teleport away, learning the location of Afterlife. Palamas reveals Ward's true plan when she helps him kidnap Morse. Gonzales leads a delegation to Afterlife to meet Jiaying and index the community. Raina foresees war if Jiaying meets with S.H.I.E.L.D., but it is assumed that she is lying in order to seize power. When Jiaying and Gonzales meet, she delivers Cal into S.H.I.E.L.D. custody, before killing Gonzales and shooting herself to start a war with S.H.I.E.L.D., rather than letting her people be indexed.

Coulson realizes that Jiaying intends to set off a war, but tries to avoid launching a counter attack for fear of hurting Skye. Meanwhile, Skye appeals to Jiaying to reconsider, and Grant tries to give Kara closure.

Coulson leads an assault on the captured helicarrier, taking Cal along with them. Meanwhile, Jiaying prepares to unleash the Terrigen crystals on the world, and Skye is forced to confront her mother.

After developing metal-melting abilities, Joey Gutierrez is saved from the hostile Advanced Threat Containment Unit by S.H.I.E.L.D. agents. When Agent Daisy Johnson struggles to explain to Gutierrez their Inhuman heritage, activated by exposure to the recently released compound Terrigen, she seeks the help of Lincoln Campbell, who taught her but now wants to live a normal life. S.H.I.E.L.D. Director Phil Coulson finds the leader of the ATCU, Rosalind Price, and the two realize that there is a third party interested in new Inhumans: the monstrous Inhuman Lash, who attacks Johnson and Campbell. The subsequent arrival of the ATCU causes both Lash and Campbell to flee. The President officially announces the ATCU as the replacement of the underground S.H.I.E.L.D., and they begin hunting Campbell. Agent Leo Fitz acquires an ancient Hebrew scroll describing the Kree Monolith, that consumed his partner Jemma Simmons, as "Death" (Hebrew: ????), which Fitz is unable to accept. Simmons, meanwhile, is on a desolate alien planet.

Dr. Andrew Garner evaluates Gutierrez and deems him not yet ready to join the Secret Warriors, Johnson's potential team of Inhumans. Grant Ward, looking to rebuild Hydra, recruits Werner von Strucker, son of previous leader Baron Wolfgang von Strucker. Tasked with hunting down and killing Ward, Agent Lance Hunter tracks down Garner's ex-wife Agent Melinda May, who has been on leave from S.H.I.E.L.D. for several months. May is convinced not to run from her life despite difficulties in her relationships with Garner and Coulson, and eventually agrees to join Hunter in his mission. Fitz realizes that the Monolith is a portal, and S.H.I.E.L.D. enlists Asgardian Elliot Randolph. Randolph takes them to an old English castle where a now-deteriorated machine was constructed to open the Monolith using vibrations. Johnson is able to replicate this effect with her abilities, And Fitz sends a flare through, before entering the portal himself. He finds Simmons and is able to bring her back just as Johnson's power destroys the Monolith.

The ATCU closes in on Campbell, who is betrayed by an old friend when the ATCU asks for public help in capturing the "alien". He calls Johnson for help. Coulson meets with Price, asking her to let S.H.I.E.L.D. take Campbell instead, but realizes that they know of Johnson too, and that to keep her safe he must let the ATCU take Campbell. Unaware of this, Johnson finds Campbell, but is followed by the ATCU. Campbell attacks them and escapes, so they try to take Johnson instead. To save her, Coulson agrees to work with Price to capture the Inhumans together. Hunter and May meet with a contact Hunter has in Hydra, who takes them to the new initiation system: Hunter must fight to the death to prove himself worthy of Hydra. Hunter fights his contact, kills him, and is accepted into Hydra's ranks. Fitz attempts to help Simmons acclimatize to her old life, but she is struggling with both the different physics of Earth, and mental trauma. Later, Agent Bobbi Morse finds Simmons wanting to reopen the portal and return to the planet.

Johnson discovers an encoded email at the scene of a Lash attack and traces it to Dwight Frye, an Inhuman who is negatively affected by the presence of other Inhumans that Lash has been using to find targets. May visits S.H.I.E.L.D. to warn Coulson that Hunter's mission is becoming too personal and reckless, but refuses to talk to Garner, who had left her while they were trying to rekindle their relationship. The ATCU takes Frye, with Johnson and Agent Mack allowed to go with them to see their base and Inhuman facilities. However, Lash ambushes their van, kills Frye, and injures Mack, but spares Daisy, who witnesses him transforming into an ordinary human afterward. Hunter is brought in on a mission with Hydra, but is seen by Ward and attacks him. May arrives to help, but Ward reveals Strucker is prepared to kill Garner unless Hunter and May allow him to escape. May, unable to sacrifice Garner, is willing to back off, but Hunter attacks Ward, shooting him in the shoulder as he flees. In retaliation, Strucker seemingly kills Garner.

Simmons agrees to tell Fitz of her six months on the planet. After being dragged through the portal, she found herself on an apparently sun-less, deserted planet, where she came across a pool of water and an alien life form inhabiting it, allowing her to sustain herself until she met stranded astronaut Will Daniels. Daniels had traveled through the portal with a team of scientists in 2001, when the monolith was in the possession of NASA, but over time they had been driven mad by the planet and an evil entity upon it, each eventually dying. Simmons realized that the opening of the portal can be predicted by studying the stars and alignment of the planet's moons, and over months they were able to anticipate the next opening of the portal. When they missed it, Simmons lost hope, but found solace with Daniels and fell in love with him. When they saw Fitz's flare, Simmons was able to make it to him while Daniels distracted the entity. Now, Simmons wants to reopen the portal so they can return to save Daniels, which Fitz agrees to help with.

S.H.I.E.L.D. finds Garner alive after Strucker fled the scene. Hunter is replaced by Morse on the Ward mission; she and May begin tracking Strucker. Since Johnson and Mack never made it to the ATCU facility, Coulson visits it himself, while Johnson, Mack, and Hunter believe that Price's right-hand man, Luther Banks, may be Lash. They find Banks, knock him out, take some of his blood, and sneak a camera into the facility to which he was headed. As an analysis proves that Banks is not an Inhuman, they realize that they are at the ATCU facility and witness Coulson seeing a captured Inhuman arrive in suspended animation. Price tells Coulson that she wants to 'cure' the Inhumans because she could not help her husband, who died of cancer. May and Morse trace Strucker to the apartment of Gideon Malick, with whom Strucker sought sanctuary. Malick, instead, turned him over to Hydra in exchange for a future favor. As Morse fights off the Hydra members, Strucker tells May that Garner survived his attack because Garner is Lash.

May confronts Garner who explains that while researching for S.H.I.E.L.D. he opened a ledger of known Inhumans, belonging to Johnson's late mother, which was booby trapped to release Terrigen on its reader. Inhuman abilities within Garner were unlocked, and when Garner was subsequently drawn to an 'unworthy' Inhuman, transformed into Lash, and killed him, Garner broke things off with May. Coulson joins Price for a meeting with the President about the outbreak of enhanced people, but is interrupted en route by Campbell, who has deduced that Lash must have access to the ledger. S.H.I.E.L.D. and the ATCU track down Garner and May, the latter being held hostage, and Coulson tries to talk down Garner. Garner's Lash instincts want him to kill Campbell, and after the latter attacks Lash only May is able to calm him down and return him to his human form. Campbell warns that the Lash form will soon be permanent, so May has the ATCU put Garner in stasis until their cure is complete. Coulson then spends the night with Price.

Malick knows that Ward wants access to one of Baron Strucker's vaults, said to contain the true power of Hydra. Malick sends men to kill Ward, as Ward's vendetta doesn't fit into his plans, but Ward defeats them and tortures the vault's location from them. Hunter and Morse enter the ATCU disguised as FBI agents investigating a security breach triggered by Garner's containment module. Morse discovers that the ATCU is keeping the Inhumans offsite, and are trying to make more instead of curing them. Coulson confronts Price, but she was unaware of this because her long-time business partner, Malick, had been running that side. Ward breaks into the vault and is confronted by Malick. As Fitz and Simmons realize that Daniels was sent through the portal by Hydra as a sacrifice to the entity, Malick explains to Ward that the entity is an ancient Inhuman who was banished through the portal, and Hydra was founded to return it to Earth. Malick agrees to help Ward take down S.H.I.E.L.D., if Ward helps him bring back the entity, and build an Inhuman army for it.

At dinner with Coulson, Price reveals plans to confront Malick before being abruptly sniped by Ward and dying in Coulson's arms. Promoting Mack to interim director of S.H.I.E.L.D., Coulson sets out for revenge and goes off-book with Hunter and Morse to kidnap Ward's younger brother Thomas. Fitz and Simmons go with Banks to investigate the ATCU, but Banks is killed and the two are captured by Hydra. Simmons is tortured until Fitz agrees to help Hydra return the Inhuman to Earth, while Coulson uses a phone call between the Ward brothers, where Grant attempts to justify himself and his past actions to Thomas, to locate Hydra: they have set up base at the English castle. Mack clears Gutierrez and Campbell for field duty, and mobilizes the rest of S.H.I.E.L.D. for a rescue mission. Hydra reopens the portal, and Malick convinces Ward to lead Hydra through it with Fitz, and return with the Inhuman, promising that Coulson will die when they return. Determined to kill Ward, Coulson manages to enter the portal as well.

Fitz finds Daniels and convinces Ward that they will need him to find the exit point. Mack sends May and the Secret Warriors (Johnson, Campbell, and Gutierrez) to find Simmons while he, Morse, and Hunter infiltrate the castle and secure the portal room. Simmons escapes herself after Campbell shuts down Hydra's power, and discovers several Inhumans that Malick has gathered as an army, including Garner. Simmons agrees to unleash Lash on Hydra before making her way to the others. Fitz and Daniels lead Ward to the ruins of an ancient civilization where they manage to get away, while Coulson catches up to Ward and overpowers him, forcing him to follow them. At the exit, Daniels attacks Fitz: the Inhuman had killed Daniels as Simmons escaped, and now inhabits his body. Ward attacks Coulson when he is distracted by Fitz, but Coulson uses his prosthetic hand to kill Ward, while Fitz uses a flare to destroy Daniels' body. Fitz and Coulson return to Earth, but the Inhuman secretly does as well, now inhabiting Ward's body.

S.H.I.E.L.D. agents arrive in Bogota to investigate an Inhuman who stole weapons from the police. The woman, Elena Rodriguez, is apprehended despite her super speed (with the limitation of returning to where she began moving from after one heartbeat) and reveals that she was destroying the weapons to prevent their misuse by corrupt police officers. Coulson uses the machine that restored his memories on Strucker - who is in a vegetative state following brutal treatment by Malick's men - and discovers where he contacted Malick. Coulson uses the phone there to find many of Malick's facilities, which are promptly shut down by Malick. The police kidnap Morse and Hunter using their own Inhuman, Lucio, who can temporarily petrify anyone using eye contact. Rodriguez aids S.H.I.E.L.D. in rescuing the pair, and though Lucio is captured by Hydra, Rodriguez agrees to join the Secret Warriors; she remains in Colombia, on call. Ellis informs Coulson that the new head of the ATCU will be Glenn Talbot, who will report directly to Coulson.

Talbot and Coulson meet with delegates from several countries to discuss Inhumans, accompanied by Carl Creel - a human who survived terrigenesis thanks to Hydra experimentation and whose blood Simmons believes could be used to "cure" Inhumans who have not yet transitioned. Coulson suspects that one of the delegates is an inside man for Malick and sends Hunter, Morse, and May to find out who it is. Hunter, seeing Creel acting suspiciously, discovers Talbot's son in ATCU stasis. They also discover that the Australian government has captured an Inhuman, Eden Fesi, for experimentation. Talbot turns on Coulson when Malick arrives, the latter convincing the delegates that Coulson is Hydra and that they should carry out their plans - the building of an Inhuman sanctuary - with Malick instead. May saves Talbot's son, allowing him to leave with Coulson without fear for his family. Hunter and Morse follow Malick to Russia, S.H.I.E.L.D. agents rescue Fesi, and Hive restores Ward's corpse to full strength by sacrificing several humans.

Hunter and Morse follow Malick to a decommissioned facility in Siberia, where Russian delegate Anton Petrov wishes to build the sanctuary against the wishes of Russian Prime Minister Dmitry Olshenko. Olshenko sends his attache to shut down the operation, but he is murdered by General Androvich, an opposition minister and Inhuman whose shadow is made of sentient darkforce. Malick suggests that the Prime Minister be invited to the facility himself and that Androvich be unleashed upon him. Hunter kills Petrov to protect Olshenko, while Morse kills Androvich to destroy his shadow. Olshenko, unaware of the attempt on his life, has the two arrested. Their Interpol interrogator threatens to turn them over to the Russians for execution unless they confirm that S.H.I.E.L.D. still exists, but Morse and Hunter refuse. Ellis intervenes with Coulson; they save the pair's lives on the condition that they never work for the U.S. government again. With the option of working in secret out of the field, Morse and Hunter instead choose to leave S.H.I.E.L.D.

Mack, struggling with the departure of Morse and Hunter, takes time off to be with his brother Ruben. When an online hate group called the Watchdogs uses Howard Stark-developed nitramene bombs to perform a terrorist attack on an ATCU facility, Coulson suspects that former S.H.I.E.L.D. agent Felix Blake - who had been committed to the advancement of nitramene technology and has been missing since having his back broken by Deathlok - has taken over the group. Ruben becomes disillusioned with Mack when he leaves to investigate a Watchdog base and accidentally reveals his S.H.I.E.L.D. agent status, but Mack is able to improve their relationship when he fends off a group of the terrorists that attack the brothers. Coulson takes Campbell to search Blake's known safehouses, and the two are confronted by Blake in one via hologram; he reveals that Hydra is backing him and the Watchdogs in their crusade to kill all Inhumans, and S.H.I.E.L.D. realizes that the attack was a cover for Hydra to steal something from the ATCU.

S.H.I.E.L.D. picks up an emergency call about Johnson, and finds the caller, who was shown a vision of his death by the Inhuman Charles Hinton, in time for him to learn Johnson's name before being murdered by Hydra, who capture Hinton. Johnson is able to touch Hinton first, giving her a vision of his death. Hive promises to reward Malick with "true power" for sending Ward through the portal; they use Hinton to obtain a powerful exoskeleton from a private corporation. Desperate to prove that fate is not fixed, S.H.I.E.L.D. seeks to stop Johnson's vision from playing out by sending May to find Hinton instead of Johnson, as the vision showed, but at the last minute Garner arrives, stating that he wants to say goodbye to May before he transforms into Lash for good. Subsequently, Johnson goes to the corporation, where S.H.I.E.L.D. has tracked Hydra and Hinton, and faces Malick and his exoskeleton. Hinton saves Johnson by distracting Malick, giving them both visions - hers of a S.H.I.E.L.D. agent dying in space - before dying himself.

Malick's father died in 1970, leaving him and his brother Nathaniel to lead the "religious" side of Hydra, including periodically sending a sacrificial "traveler" - chosen at random from Hydra's inner circle - through the portal for Hive to inhabit until his return. Discovering that their father used a trick to never be chosen as the traveler, Gideon does the same and Nathaniel is chosen. In the present, Gideon tells his daughter Stephanie of his vision: he believes he saw his own death at the hands of Hive. Johnson and Campbell track down James, an untransitioned Inhuman with knowledge of Hive who gives them an ancient Kree device. The rest of S.H.I.E.L.D. captures Giyera, Gideon's right-hand man who is now loyal to Hive; a telekinetic Inhuman, Giyera takes control of their plane and directs it to a Hydra base with most of S.H.I.E.L.D. as his prisoners. Hive comes to the Malicks' house and reveals to Gideon that he has Nathaniel's memories. As punishment for Gideon's betrayal of Nathaniel, Hive murders Stephanie in front of him.

Johnson and Campbell unite with Gutierrez and Rodriguez as the Secret Warriors, and infiltrate the Hydra base to free S.H.I.E.L.D. Gutierrez kills Lucio in the process, while Campbell captures Malick. During questioning, Malick explains to Coulson that Hive can infect the minds of Inhumans, warning him against trusting any of the Secret Warriors. Simmons confirms from an autopsy of Lucio that Hive parasites infected his brain, and the same could have happened to any of the Secret Warriors. When Malick is found dead, the human agents trap the Inhumans in quarantine and search their belongings. They discover the Kree device in Campbell's possession rather than in asset lockup; Campbell protests, but the other three are released. That night, Johnson visits Campbell and offers to break him out. Campbell refuses when he realizes that Hive is controlling Johnson, and used her to murder Malick and frame Campbell. Johnson leaves on her own, creating an earthquake to destroy the S.H.I.E.L.D. base with everyone inside.

Escaping the base mostly unharmed, S.H.I.E.L.D. knows that Johnson could have killed them all, and believe there is hope of freeing her from Hive. Fitz and Simmons seek out transhumanist Holden Radcliffe, who believes in the improvement of humanity through enhancement, and whose studies of parasites could help with counteracting Hive's abilities. Hive turns Alisha Whitley (a duplicating Inhuman ally of S.H.I.E.L.D.) and James (after first giving him terrigen which allows him to imbue objects with fire) to his cause, and takes this fledgling army to interrupt Fitz and Simmons: Johnson warns Fitz of her vision; Hive's memories of Daniels petition Simmons to move on with her romantic life; and the others kidnap Radcliffe, taking him to a town that Hive bought with Malick's remaining fortune, where he intends to recreate the original Kree experiments that made the Inhumans. Talbot and the ATCU use Malick's final intel to completely dismantle Hydra's remaining infrastructure, and Fitz and Simmons finally consummate their relationship.

Radcliffe's first attempt to turn humans into Inhumans fails, as he requires Kree blood. Fitz and Simmons attempt to combine their potential Inhuman cure with what they know of Radcliffe's research, but require an Inhuman test subject; Campbell volunteers himself, severely compromising his immune system, and seemingly proving that the cure cannot free the Inhumans of Hive's connection. S.H.I.E.L.D. locates the town, and Mack and May lead a team to hopefully free the others by simply killing Hive. The latter activates the Kree artifact, a beacon which calls two Kree reapers to the town. They promptly murder Whitley. Johnson and Hive confront a reaper each, with Johnson managing to begin harvesting hers' blood until the process is sabotaged by Mack. Hive, not realizing this, destroys the other reaper. Johnson attacks Mack, nearly killing him, but is interrupted by May, who helps Mack retreat with the rest of their team. Johnson then offers her own blood as an alternative for Radcliffe's experiment, as it was recently infused with Kree blood.

Following the signing of the Sokovia Accords, Talbot and Coulson discuss registering the Inhuman agents, with Coulson taking Talbot to the S.H.I.E.L.D. base to introduce him to Rodriguez and Lash, explain the Hive situation, and show him the need to keep the Secret Warriors anonymous. Hive captures several Watchdogs for Radcliffe's next experiment attempt; they are horrifically mutated into primitive Inhumans, but do fall under Hive's sway, prompting him to proceed with his ultimate plan - to use a warhead (what was stolen from the ATCU) to spread Radcliffe's new pathogen around the world and transform all humans into these primitives. Campbell contacts Johnson and convinces her that he wants to be with her. Hacking into S.H.I.E.L.D.'s systems as her blood is drained, Johnson helps him escape the S.H.I.E.L.D. base in a quinjet. However, this was a ruse on S.H.I.E.L.D.'s part, with Lash arriving instead of Campbell. Lash uses his abilities to free Johnson from Hive's sway, but is killed by James. Johnson escapes back to S.H.I.E.L.D.

S.H.I.E.L.D. keeps Johnson in containment while she is showing withdrawal symptoms after losing her connection with Hive, but her intel allows them to find the base where Hive is attempting to launch the warhead. With Talbot's military contacts S.H.I.E.L.D. is able to disable the rocket, while a team of agents infiltrates the base, captures Hive, and extracts Radcliffe, with the latter agreeing to cooperate with S.H.I.E.L.D. and revealing that the Primitive process is irreversible. Giyera and James steal the warhead, and while S.H.I.E.L.D. is focused on locating it, they detonate a bomb that they had smuggled into the S.H.I.E.L.D. base which releases some of Radcliffe's pathogen. Several S.H.I.E.L.D. agents transform into Primitives and free Hive from his containment, and he proceeds to steal Zephyr One, S.H.I.E.L.D.'s airborne mobile command that could take the warhead high enough for the pathogen to transform most of humanity. Johnson escapes and confronts Hive, begging him to connect with her again.

Hive realizes that Lash has made Johnson impervious to his influence, and so instead overpowers and abducts her. Giyera and James bring him the warhead, while many of the Primitives remain to kill the rest of S.H.I.E.L.D. May and Fitz infiltrate Zephyr One and free Johnson. Fitz kills Giyera, while Coulson and the others evade the Primitives and escape the base in a quinjet, boarding Zephyr One. Coulson plans to send the warhead into space in the quinjet to detonate safely, and Johnson believes that she must go with it to atone for her actions under Hive's sway, and fulfill her vision. She enters the quinjet where she is confronted by Hive, but Campbell throws her out and overrides the jet's controls, ascending to space, where the warhead detonates and kills both him and Hive (fulfilling Johnson's vision anyway). Six months later, Johnson has left S.H.I.E.L.D. and is operating as the vigilante "Quake", evading Coulson, who is no longer director of S.H.I.E.L.D. Radcliffe turns his artificial intellegence AIDA into a Life Model Decoy.

Former S.H.I.E.L.D. agent Daisy Johnson, now the vigilante "Quake", is hunting gang affiliates of the terrorist group Watchdogs in Los Angeles when Aryan Brotherhood members are murdered by the fiery "Ghost Rider". Agents Phil Coulson and Mack, who were forbidden from searching for Johnson by new S.H.I.E.L.D. Director Jeffrey Mace, are tipped off to her location by Agent Melinda May. Agent Leo Fitz discovers that S.H.I.E.L.D. ally Holden Radcliffe has created the android AIDA, and agrees to help perfect her. He keeps this from his girlfriend Agent Jemma Simmons, who is in the Director's inner circle. Simmons discovers that Coulson and Mack are investigating Johnson, and orders May to stop them. She arrives to find them surveilling Chinese gangsters who bought a weapon off the Brotherhood: a mystical figure, who turns the gang members berserk, and secretly infects May as well. Johnson tracks down the Ghost Rider, but he defeats her. She later sees his human form, Robbie Reyes, looking after his disabled brother Gabe.

S.H.I.E.L.D. and Johnson independently investigate the figure, an apparent ghost of a woman named Lucy Bauer, both concluding that she worked at an abandoned facility, Momentum Energy. Johnson confronts Reyes again, and he once more overpowers her. Restraining her, Reyes searches Johnson's belongings and discovers her research on Momentum. He leaves, and Johnson escapes her restraints. As Mace plans to officially announce S.H.I.E.L.D. as a legitimate organization again, the infected May grows increasingly paranoid, seeing all people as monsters, and eventually attacking other agents. Mace restrains May with his Inhuman strength, and promises to take care of her. Mack and Fitz arrive at Momentum to find more ghosts, who attempt to blow it up with them inside. Ghost Rider intervenes, destroying one of the ghosts, and Johnson arrives to stop S.H.I.E.L.D. from taking him in. Rather than rejoin S.H.I.E.L.D., Johnson agrees to work with Reyes, who believes that the actions of the ghosts and Watchdogs may be tied to him.

Inhuman S.H.I.E.L.D. asset Elena Rodriguez is caught in a blackout in Miami. Reyes and Johnson are caught in another in Los Angeles. A group claiming to be the Inhuman resistance, fighting registration with the Sokovia Accords, take responsibility. Reyes explains that his uncle, Eli Morrow, was imprisoned for causing an explosion at Momentum that apparently created the ghosts; he believes that atoning for Morrow's sins will pay his debt to the Devil, and rid Reyes of the Ghost Rider. At the Reyes' house, Gabe realizes that Johnson is Quake and asks her to leave Robbie alone. Radcliffe and Simmons "cure" May by killing and reviving her. Coulson, Mack, and Fitz save Rodriguez from a group of Watchdogs, and find the EMP that caused the blackout - it was set off by the Watchdogs, who had access to S.H.I.E.L.D.'s list of registered Inhumans, and have backing from Senator Ellen Nadeer, whose brother is encased in an Inhuman terrigen cocoon. Hoping to assuage public fears of the Inhumans, Mace announces the return of S.H.I.E.L.D.

Johnson forces Simmons to help track the Watchdogs' actions. They discover that the group hacked an Inhuman's monitoring device, and race to save the next Inhuman on the list. Coulson visits Morrow in prison, but gets no answers. Reyes arrives to talk to Morrow, and Mack recognizes him as the Ghost Rider. They capture Reyes, and earn his trust. AIDA supervises May's recovery, as a Turing test by Radcliffe. Johnson and Simmons find the Inhuman J.T. James and destroy his monitor. Reyes visits Morrow, and learns that the Momentum explosion was caused by a group of scientists studying the Darkhold, a mysterious book. Only Lucy's husband Joseph, whom Morrow had put in a coma trying to stop the experiments, survived. James betrays Johnson - he hates being an Inhuman, and gave the Watchdogs access to his monitor. Coulson, Mack, and Reyes save Johnson and Simmons, alerted by the monitor's destruction. They then get May to help find the Darkhold, and when Simmons sees AIDA she deduces her true nature.

Lucy wakes Joseph to find where he hid the Darkhold. Coulson arrives, and is able to learn of this before Joseph dies from her ghostly infection. Coulson decides to use Morrow against Lucy, but doesn't tell Mace. The latter, whose public approval was high after heroics during a bombing in Vienna, becomes more popular after he reveals his Inhuman status in a television debate with Nadeer. Mace exempts Simmons from any lie-detection tests after she threatens to reveal the truth about Vienna to keep AIDA secret. At the prison, Lucy infects the staff, who attack Coulson and May. Johnson saves them while Mack and Reyes break Morrow out. Reyes confronts the last member of the "Fifth Street Locos" gang who had paralyzed Gabe in a paid hit. Reyes loses control, and the Ghost Rider kills the prisoner. This allows Lucy to kidnap Morrow, whose help she needs in becoming human again and finishing their work. Mace secretly meets with Nadeer, who threatens to release footage of Ghost Rider killing the prisoner while working with S.H.I.E.L.D.

Mace sends Simmons on a secret assignment, then takes a team to board the Zephyr and arrest Reyes and Johnson. The pair hides with a newly picked up Gabe, explaining that he had convinced Gabe to sneak out with him to race in Morrow's car, but they were attacked by the Fifth Street. Gabe was paralyzed and Reyes was killed before he promised an unknown voice that he would kill the people who murder innocent people in exchange for being revived, and came back to life as another Ghost Rider passed him that power.[N 1] Mace finds the fugitives, but agrees to let Coulson use Reyes against Lucy after the Ghost Rider overpowers the former in a fight. Fitz tracks Lucy to an abandoned Roxxon power plant, where Reyes kills her after she reveals that Morrow craves the Darkhold's power himself - he had intentionally created the ghosts, and Joseph had ordered the hit on Morrow's car to try to stop him. Morrow activates an improved version of the Momentum machine and gains the power to create matter. Reyes, Fitz, and Coulson disappear from the facility.

Coulson, Fitz, and Reyes are trapped between dimensions, and helplessly watch as Morrow kills several agents and escapes. Fitz overhears Mace arguing with Nadeer; he needs Simmons to understand Morrow's technology, but she has been taken to Nadeer's brother, who she helps escape from his terrigen cocoon. In Simmons' absence, Radcliffe studies the technology, and is presented with the Darkhold by May in her desperation to save Coulson. Radcliffe believes the book contains too much knowledge for a person to process, but Aida is able to read it, revealing her android nature to Coulson and May. Aida constructs a portal through which Coulson and Fitz return. During this time, the Ghost Rider spirit had left Reyes and possessed Mack to avoid the other dimension, where it had been before. Reyes confronts the spirit, promising to serve it even after they defeat Morrow if it leaves Mack. It agrees, and Reyes returns with it through the portal. Secretly, Aida begins experimenting with her new knowledge from the Darkhold, creating an artificial brain.

Coulson tells Mace that Aida is an android, and he agrees to use her to fight Morrow. He also approves a strike team consisting of Rodriguez, Reyes, and Johnson, as long as the latter two keep a low profile. The team attempts to enter an abandoned building that Morrow has barricaded himself in using his growing abilities, but at first only Reyes can make it through one of Morrow's traps. Seeing through a camera on Reyes, Fitz deduces that Morrow draws his power from the other dimension, and has created a demon core which could destroy half the city if activated. Aida creates a new dimensional portal beneath the demon core, through which the device and Morrow are dragged. Reyes also falls through the portal after using the Ghost Rider to hold Morrow in place. Johnson is seen by local media, and Mace publicly clears her name, reinstating her as an agent of S.H.I.E.L.D. He then allows Radcliffe to continuing working on his Life Model Decoy (LMD) program given the success of Aida, though she has secretly replaced May with an android LMD.

Fitz and Radcliffe are sent to clear Aida's memory of the Darkhold, but she reveals her new-found sentience and overpowers them. Taking control of S.H.I.E.L.D.'s systems, Aida finds the Darkhold after Coulson gives its location to the May LMD (which doesn't know it isn't the real May). Fitz is able to take control of the systems before Aida escapes, and Mack "kills" her. Radcliffe later laments about this to a new model of Aida, as he had programmed the original's apparent sentience in an attempt to steal the Darkhold for himself. Senator Nadeer orders a group of Watchdogs to kill a now recovered Vijay, but he convinces her to spare him as his long terrigenesis appears not to have affected him. Simmons, having identified Vijay from photographs, Mace and Johnson arrive, as Vijay discovers he now has super-reflexes. Ellen convinces him to leave with her, but then shoots him in the stomach. Ellen asks the Watchdogs for reinforcements from "The Superior" as Vijay's body is dropped into the ocean and enveloped by another terrigenesis cocoon.

Mace holds a press conference for Johnson, celebrating her "undercover" actions, until a sniper attempts to assassinate Mace. Coulson and Mack escort Mace and PR agent Burrows - who is often seen near Mace with a mysterious briefcase - to a quinjet, but it explodes mid-flight. Burrows is flung from the plane with the briefcase, and the others crash land in a forest. There they find ex-Hydra agents, hired by the Watchdogs, who have recovered Burrows' body. In the ensuing fight, Mace tries to get a serum from the briefcase, but it is destroyed and he is injured. Mace explains that he is not an Inhuman, and was given his abilities by a super-serum from the government to create a trustworthy enhanced individual to lead S.H.I.E.L.D. After their rescue by Johnson and the May LMD, Coulson tells Mace to continue as "the Patriot", the face and political leader of S.H.I.E.L.D, while Coulson takes back command of operations. The May LMD discovers her robotic skeleton from a wound, and Fitz secretly begins studying Aida's decapitated head.

Johnson and Mace attend a Senate hearing to ratify the former's signing of the Sokovia Accords, with Senator Nadeer questioning Johnson's undercover actions. Coulson and Rodriguez infiltrate Nadeer's office to install surveillance devices, but are caught, giving Nadeer an excuse to start a full investigation of S.H.I.E.L.D. The May LMD realizes that she had subconsciously leaked the details of Coulson's plan and confronts Radcliffe, as Fitz discovers Radcliffe's treachery from the original Aida's programming. Radcliffe explains to the LMD that her programming will not allow her to reveal her nature to anyone else, before S.H.I.E.L.D. arrives and arrests him. Fitz later confronts Radcliffe in his cell and deduces that he is also an LMD - the real Radcliffe had sought protection from Nadeer after Aida's initial failure. He and Aida have May captive with them, her mind in a virtual reality simulation of a tragic past event. Meanwhile, Mack and Rodriguez have grown close, and he tells her of his daughter Hope, from a past marriage, who died as an infant.

Agent Billy Koenig, who Coulson entrusted with the Darkhold, is abducted by the Watchdogs. Nadeer directs Radcliffe to the Superior, reclusive industrialist Anton Ivanov, and Radcliffe scans Koenig's brain to learn that the Darkhold was hidden in the Labyrinth, a S.H.I.E.L.D. facility known only to the Koenig family. Coulson secures the rest of the Koenig family, who take him, the May LMD, and Johnson to get the book. The Radcliffe LMD reveals that Radcliffe knows Fitz's estranged father, and has created another LMD. Simmons remembers that Radcliffe scanned May's brain when they were curing her of Lucy's influence, and warns Johnson of the May LMD in time to stop it from taking the Darkhold and killing Coulson. The Watchdogs arrive with Billy, and Radcliffe steals the Darkhold in the ensuing fight. S.H.I.E.L.D. later destroys the remains of the first Aida and the Radcliffe LMD. Ivanov explains to Radcliffe that he plans to use the Darkhold to destroy both the Inhumans and the man who appears to be behind the recent alien crises - Coulson.

Coulson and Mack locate Agnes Kitsworth, Radcliffe's former lover and partner. Radcliffe left Kitsworth after she was diagnosed with terminal cancer, and modeled Aida after her. Coulson convinces Kitsworth to meet with Radcliffe. In case Nadeer is an Inhuman like her brother, Ivanov sends Watchdog Tucker Shockley to expose her to terrigen (provided by Radcliffe), but the substance transforms him instead. Shockley explodes, killing Nadeer, and then his molecules reassemble. Ivanov agrees to use Shockley's new ability against S.H.I.E.L.D. Radcliffe meets with Kitsworth and convinces her he can save her life if she escapes with him before S.H.I.E.L.D. captures them. Johnson confronts Shockley, and distracts him long enough for Fitz and Simmons to contain him in a specially-made device. Ivanov uses this as a distraction to attack and kidnap Mace, who has learned that each time he uses his super-serum there is a chance that it will kill him. As Kitsworth dies of the cancer, Radcliffe places her consciousness in the virtual "Framework" with May.

Years ago, Coulson and May recovered an unknown object from a Russian outpost, besting an SVR team that included Ivanov. For the failure, the SVR agents other than Ivanov were tortured and killed. Now, Ivanov leads S.H.I.E.L.D. on a treasure hunt around the world, including to that outpost, in their search for Mace. Ivanov has been torturing Mace, disgusted at his attempts to emulate the Inhumans. The team eventually finds Ivanov, and Johnson overpowers him. Coulson and Mack save a near-death Mace while Fitz and Simmons attempt to locate any sign of the Framework in hopes of finding May. Unsuccessful, the pair reunite with the others and they return to base. Aida, whom Radcliffe has left to carry out his plans while he spends time in the Framework, finds a crippled Ivanov. At base, Fitz and Simmons are alerted by their LMD security system, learning that four agents were replaced with LMDs by Aida while Fitz and Simmons were separated from the group. This includes Coulson, as the Coulson LMD wakes the May LMD from storage.

The new LMDs are aware of their nature, and plan to carry out Ivanov's goal of destroying all Inhumans. Simmons soon discovers that Mace, Mack, and Fitz are the other new LMDs, and overpowers Fitz. Johnson also discovers the subterfuge, and plans with Simmons to escape the base and hack into the Framework remotely to find the others from the inside. Johnson overpowers the Mace, Mack, and Coulson LMDs, while Simmons recruits other S.H.I.E.L.D. agents. They find the May LMD waiting for them at the base entrance, tasked with detonating a large explosive to prevent their escape. The May LMD instead lets them leave, and destroys the base with the LMDs inside. In the Framework, the agents find an altered reality: Johnson is in a relationship with an alive Grant Ward; Coulson is teaching about Inhumans; Mack's child is alive; Fitz is rich; Simmons is dead; and May works for Hydra, which has replaced S.H.I.E.L.D. In the real world, Aida severs Ivanov's head from his crippled body and builds an android body for his mind to control.

In the Framework, Johnson discovers that she and Ward are agents of Hydra, working under May and Fitz. The tragic event from May's past has no longer happened; in the real world she killed a young Inhuman girl, but in the Framework she brought the girl back to America as a refugee, who then became a mass murderer and the catalyst for Hydra to take power. Simmons awakens in a mass grave of S.H.I.E.L.D. agents, and eventually comes across Coulson who is teaching a Hydra-approved curriculum that warns against the dangers of Inhumans. Simmons is unable to convince Coulson that he is inside a virtual simulation, and he calls Hydra. Johnson races to find Simmons before the rest of Hydra, and is followed by Ward, who reveals himself to be a mole inside Hydra for the Resistance. Johnson and Simmons try to exit the Framework using a safeguard the latter created, but it has been blocked by Aida, who has entered the Framework as the Director of Hydra and Fitz's lover. Johnson then goes to Coulson, and he remembers her name.

Hoping Radcliffe can help them escape, Johnson returns to Hydra and locates him, but May gives her a new mission on the orders of Fitz and Aida, the latter choosing to go by Ophelia, or Madame Hydra. Ward directs Coulson (who can remember some things, thanks to previous tampering with his mind) and Simmons to the Resistance, the remnants of S.H.I.E.L.D. under the command of an Inhuman Mace. Ward, Simmons, and Coulson take a stolen Hydra quinjet to extract Radcliffe. May and Johnson arrest Mack, and May forces him to trick Johnson into confessing her true allegiance. The others find Radcliffe living in seclusion with Kitsworth, and he explains that he and Kitsworth cannot leave the Framework due to their real bodies having died. Fitz and Madame Hydra arrive, and Radcliffe attempts to appeal to Fitz, though Fitz already knows of the "other world" and that Radcliffe had enslaved Aida there. He kills Kitsworth and imprisons Radcliffe, torturing him and Johnson. Regretting his actions, Mack joins the Resistance.

Mace and Coulson infiltrate a Hydra "Enlightenment Camp" to free an undercover agent—Antoine Triplett, a S.H.I.E.L.D. agent who died in the real world. They are tracked there by May, who uses a super serum to fight Mace. Through the vents in their holding cells, Daisy learns from Radcliffe of a backdoor he installed to escape the Framework that Aida is unable to disable. Coulson attempts to save one of his former students who he sees being held in the camp, and Mace follows him into a building to help. Hydra uses a missile to bring the building down, and May enters the rubble to ensure Mace is dead. She finds him stopping debris from crushing the student, with Coulson and Triplett helping other children escape the building. May is horrified to find children being victimized by Hydra. With the others to safety, Mace is crushed beneath the debris, and in the real world Aida finds his physical body dead as well. Turning on Hydra, May sneaks a Terrigen crystal to Johnson so she can gain her Inhuman abilities within the Framework.

May and Johnson escape Hydra, with Johnson using her abilities to break Ophelia's back. Ophelia insists that Fitz complete work on their secret Project: Looking Glass, after which her Framework body will no longer matter. May and Johnson join up with S.H.I.E.L.D., who are struggling to regroup after Mace's death. May provides them with body cam footage from the attack on the Enlightenment Center, which Coulson broadcasts to the world to counteract Hydra's propaganda. Meanwhile, Simmons and Triplett investigate a Russian oil platform which he believes is the location of Looking Glass from his time undercover; the platform is the Framework equivalent of Ivanov's oil platform in the real world, from where Aida is running the Framework. The pair find the platform empty, and Simmons deduces that Looking Glass consists of a machine built on the real world platform, to be connected to a machine in the Framework using knowledge from the Darkhold, allowing Ophelia to go from the Framework to a true human body in the real world.

After Johnson and Simmons entered the Framework, their bodies were protected by Rodriguez aboard the S.H.I.E.L.D. aircraft Zephyr One. With their connection to the Framework draining the plane's power, Rodriguez chose to shut off its cloaking ability, revealing their location to Ivanov and his men. In the Framework, Simmons visits and accidentally kills Fitz's father Alistair, and Fitz begins hunting her with help from Radcliffe (Fitz offers to send Radcliffe through the machine, restoring his living body). Ophelia initiates her transference into her new body. Johnson takes the group to Radcliffe's exit point, where she, Coulson, and May cross back into the real world. Fitz arrives and confronts Simmons, but is overpowered by Radcliffe, who regrets all his actions since he first saw and wanted the Darkhold. Radcliffe sends Fitz through, followed by Simmons. Mack decides to stay, not wanting to live in a world without Hope. At Ivanov's platform, the newly human Ophelia confronts Coulson, May, and Fitz, teleporting away with the latter.

The agents on Zephyr One fight off Ivanov's men and race to the platform to save Coulson and May from Ivanov's android bodies. Ivanov launches torpedoes at the platform that threaten Mack's body, but the latter is saved by Ophelia, convinced by Fitz to put to good use the Inhuman abilities his machine had given her new body. In isolation at S.H.I.E.L.D., Fitz and Ophelia discuss her newly discovered human emotions and the fact that he remembers all the terrible things he did inside the Framework. He admits that he ultimately still loves Simmons over her, outraging Ophelia. Talbot arrives at the ruined S.H.I.E.L.D. base, where Ophelia kills several of his soldiers and other S.H.I.E.L.D. agents. Coulson and the others flee in the Zephyr once more, while Ophelia returns to Ivanov, who plans to use knowledge from the Darkhold to apply the changed reality of the Framework to the real world. Meanwhile, Rodriguez enters the Framework herself to try convince Mack to leave, and the Ghost Rider returns through a portal from the other dimension.

Ivanov takes the Darkhold to an international meeting on S.H.I.E.L.D. and the recent events. He proposes to use the book against the Inhumans, which is timed with an attack on the group by an LMD of Johnson, who shoots Talbot in the head leaving him comatose. In the ensuing fight, S.H.I.E.L.D. is able to retrieve the Darkhold with Reyes' help. In the Framework, Rodriguez is unable to convince Mack to leave, but he returns with her after Hope's code is deleted as a result of Ophelia shutting down the Framework. Radcliffe is also deleted, after accepting that immortality without Kitsworth would not have been worth it. Ophelia comes for the Darkhold, and Coulson surprises her by unleashing the Spirit of Vengeance himself, having made a deal to become the Ghost Rider for a short time. He incinerates Ophelia. Reyes, now the Ghost Rider again, takes the Darkhold through a portal. The S.H.I.E.L.D. agents then wait to be arrested by the government, but are instead taken by a mysterious group. Some time later, Coulson is working on a space station.

Enoch, an alien, leads a team of commandos to apprehend Coulson and his team after they were framed for the attempted assassination of General Talbot. While Fitz is left behind, the rest are taken to an unknown location. A white monolith transports them to an outpost in an unknown region of space, where a group of scavengers are under attack from aliens they call "roaches." One of the scavengers, Virgil, tries to explain their situation to Coulson, but is quickly knocked out by Mack. Yo-Yo and Simmons find Coulson and Mack. Coulson finds an old postcard in Virgil's jacket. Virgil recognises each of the S.H.I.E.L.D. agents when he regains consciousness. As he begins to explain that he studied their history, he's suddenly killed by one of the roaches. While Daisy saves the team, May is injured and sees Deke, another scavenger. May attacks him but is overpowered. He ties her up and implants a device called a "metric" into her wrist.

The team finds May's jacket and realise the outpost appears to be a human colony. They find a computer, however, triggering an alarm that sends a team of Kree Reapers right to them. The Kree take Daisy, Coulson and Simmons to a prison, while Mack and Yo-Yo are tied up and tortured. Deke shows up at the prison with May, and convinces the Kree to let them hand over their prisoners to him. Deke tells them Virgil hired him to swap out the team's metrics so the Kree wouldn't notice them. With Virgil dead and the team unable to cover what he's owed, Deke attempts, but May grabs one of Deke's gadgets he used against her earlier to pin him to a wall.

May and Simmons follow Deke's directions to a ship that could send a message to Fitz to rescue them, Daisy heads off to find Mack and Yo-Yo, and Coulson stays behind to get information out of Deke. Daisy frees Mack and the two set out to save Yo-Yo. Gradually, all of them come to realise that the monolith didn't take them into space, but to a future where the Earth has been destroyed, and the outpost is all that remains of humanity. Mack finds a message on the postcard reading "Working on it - Fitz".

May and Simmons return to the outpost, where Deke offers to give implant metrics in their wrists so they can blend in. They're suddenly interrupted by Tess, another scavenger, and Deke tells her about Virgil's death. Deke leaves to find Daisy, Mack, and Yo-Yo once Tess offers to double what Virgil owed him, while Tess takes the rest of them to the Exchange, humanity's main living area on the outpost. The outpost, known as the "Lighthouse", was a survival bunker when the Earth was torn in half by a cataclysmic event. The Kree arrived to restore order, and destroyed the historical records to keep humanity focused on their future. Although the Kree often abuse their human subjects, they rely on the Kree for survival.

Tess takes Coulson to Virgil's apartment, where Coulson finds a notebook Virgil hid among the artifacts of the old world he collected. Tess' boss, Grill, confronts her about the ship May and Simmons took out earlier, and says she owes him double now that Virgil is gone. May and Simmons witness one of the Kree's human servants getting stabbed in the fight. The Kree take Simmons away when she looks after his wound rather than let him bleed out. Deke, Daisy, Mack and Yo-Yo meet up with Tess, Coulson and May in the Exchange after they dispose of the Reapers' bodies. Suspicious of Deke's motivations, Daisy follows him to his "gallery", where people pay to enter a Framework simulation to escape the brutal reality of life in the Lighthouse. Daisy passes out when she walks under Deke's transmitter, and finds herself in a simulation with Deke.

The Kree take Simmons to see Kasius, the overseer of the Lighthouse. Kasius orders his enforcer Sinara to begin a "renewal" among the humans. Back in the Exchange, Coulson, Mack and Yo-Yo steal a tablet from a Kree, and give it to Grill in exchange for implanting their metrics. The renewal begins while they are in Grill's shop. The Kree select a group of low earners, each of which will either have to be killed or kill another before the renewal ends. One scavenger sets out to kill Grill for not paying him earlier. Grill leaves Coulson, Mack and Yo-Yo behind as decoys while he goes into hiding. May tries to fight the scavenger off, only for Tess to grab the shotgun and kill him instead. Grill claims the team work for him when a Kree watch commander comes by to check on the renewal's end.

Kasius demands perfection from anyone who represents him, and has Sinara kill the servant. Kasius places a liquid into Simmons' ear, causing her to lose her hearing. Meanwhile, Daisy confronts Deke about using the Framework. Deke reminds her that the Earth is gone and humanity is near extinction. Deke pauses a TV playing a news report about Daisy saving Los Angeles. He went into the Framework to confirm that Daisy was Quake, the person he believes tore the Earth apart. Later, Simmons becomes Kasius' servant, whose voice is the only one she can hear.

In preparation for Lady Basha's arrival, Simmons is given the task of helping an Inhuman champion control her abilities for her exhibition ceremony. Simmons is successful but becomes distraught when Kasius sells his champion to Lady Basha. While the team adapt to their new jobs, Grill becomes suspicious of the new arrivals and sends one of his men to spy on them. During a space expedition, Coulson, May, Mack, and Tess struggle to make sense of Virgil's notebook and discover a radio transmission supposedly originating from the Earth's surface. Grill's spy reports back, only to be framed as a traitor and exiled to die on Earth. Meanwhile, Yo-Yo helps Johnson get ahold of a Kree tablet to try and save Simmons. However, her mission is thwarted by Deke, who reports her to Kasius. Johnson is captured and taken to become his new champion.

Johnson meets Ben, one of Kasius' other champions, capable of telepathy. Using Ben to corroborate their story, Kasius interrogates Johnson and Simmons about the others. They are able to convince Kasius they came alone, though he remains suspicious. During the interrogation, Ben learns that Kasius intends to destroy the station and everyone on it once he acquires enough profits to leave. Deke returns to the others to gather new information as they learn about the mysterious Level 35. Recognizing his father's voice on the radio transmission, Deke agrees to help them gain access to the restricted floor. There, they discover that Kasius is attempting to breed Inhumans. May also discovers Deke lied about Johnson's whereabouts, but get interrupted by Sinara's arrival. Coulson leaves with Deke, while May fights her alone. Meanwhile, Grill sends Mack to confront someone who owes him payment. Later, Fitz is revealed to be one of the bidders who have arrived for Johnson's exhibition.

Shortly after the others are taken from the diner, Fitz is taken into military custody and interrogated by General Hale and her subordinates about the others' whereabouts, as well as their involvement in the assassination attempt on General Talbot and deaths of Jeffrey Mace and Holden Radcliffe. For the next six months, Fitz is given special privileges to allow him to locate the team, but he fails. With help from Lance Hunter, Fitz escapes the military facility and tracks down Enoch, the man who took the others. Enoch explains that a prophecy foretold these events and takes them to meet Robin, the daughter of Charles Hinton, who expresses her prophetic abilities through drawings. Tracked by the military, Enoch helps them escape to a secret bunker, where Fitz learns that he was left behind so he could save the team. Determined to help them, Fitz and Hunter break back into the same military facility to obtain a cryogenic pod; they find all their old S.H.I.E.L.D. tech, including the Zephyr, which they use to escape. Using the pod, Fitz is put to sleep for the next 74 years. He is awoken by Enoch, who prepares him for their arrival at the Lighthouse.

Down in the station, the Kree have harvested some of the youth for an unscheduled terrigenesis ceremony. Flint, a friend of Tess, experiences a successful terrigenesis and is taken into hiding with the team by Yo-Yo. Tess is killed and hanged for Flint's disappearance. During a dinner with the other bidders, Fitz quickly proves himself as a formidable character, earning Kasius' respect. The first exhibition is then held between Ben and May, resulting in May being sent to the surface, while Ben is killed for lying during Johnson's interrogation. Meanwhile, Grill finds the team and holds them captive, until Flint saves them using geokinesis against Grill, killing him. The unexpected arrival of Kasius' brother prompts Sinara to battle Johnson for her exhibition. During which, Johnson, Fitz, and Simmons are able to subdue the others and escape. During the escape, Simmons proposes to Fitz.

Johnson, Fitz, and Simmons are hunted throughout the station and discover the station is being sustained by gravitonium. Fitz is shot during the chase. Deke finds them and takes them to the rest of the team. Reunited, the team plot their escape to the Earth's surface by using a trawler and Deke's antigravity device. After learning about Tess' death, Flint decides to stay on the station to protect the remaining inhabitants. Mack and Yo-Yo agree to stay behind and help him. Coulson, Johnson, Fitz, Simmons, and Deke fly to the surface, but get caught in the gravity storm. Meanwhile, Kasius kills his brother and plots to regain his father's acceptance by recapturing Johnson with help from Sinara. On the surface, Enoch finds May, but their meeting is cut short by the approaching gravity storm. A mysterious figure takes them to safety, where they are greeted by an elderly Robin.

Coulson, Johnson, Fitz, Simmons, and Deke survive the crash and reunite with May in the Zephyr. They meet Samuel Voss, an acquaintance of Deke's father. Up on the Lighthouse, Kasius punishes the inhabitants by cutting off their resources. Flint, Mack, and Yo-Yo go to retrieve the weapons hidden by Fitz and discover Kasius has released the Vrellnexians onto the lower levels. They defeat the Vrellnexians and rescue the remaining inhabitants. On the surface, the team struggle to get answers from Robin and find a machine built into the Zephyr. While Fitz and Simmons attempt to remove Johnson's inhibitor, May and Coulson find a shard of the time monolith in Voss' locker. Deke questions Voss about the shard, which belonged to his parents, and gets knocked out. Voss then tries to kill Johnson and impales Robin to prevent her from giving the team answers. Before dying, Robin is comforted by May as she reveals their history and finally tells May how to save the world, which requires Flint. In the past, May is shown taking care of Robin and encouraging Fitz to build his machine so they can travel through time.

As the gravity storm worsens, the team attempt to relaunch the Zephyr. May reveals that using the shard, Flint can recreate the monolith allowing the team to travel back through time. Similar to the Lighthouse, Fitz and Simmons find gravitonium on the Zephyr and realize the designs were manufactured by Fitz himself. On the station, Flint, Mack, and Yo-Yo successfully gain control of the lower levels. Tess is resurrected by Kasius and sent to relay demands for him, who threatens to detonate explosives killing everyone if they are not met. Mack and Yo-Yo retaliate by placing the explosives on Level 35, the medical floor, which would prevent Kasius from breeding more Inhumans. During a standoff with Kasius, Flint evacuates the inhabitants to the upper levels and uses the remaining explosives to separate them from the lower levels, out of Kasius' reach. Using the gravity storm to her advantage, May navigates the Zephyr into space as Johnson battles Sinara again, this time killing her. Johnson then contacts Mack while the team are heading for the Lighthouse. Kasius reveals he has his own seer telling him what will happen.

While Enoch stays on the Zephyr, the team focus on getting to Flint and rescuing the other Inhumans from captivity. Distraught over Sinara's death, Kasius infects Tye, the Inhuman trainer, with odium, a substance that excites maniacal behavior and sends him after the team. During a fight with Tye, Coulson seemingly gets infected. Kasius' seer is revealed to be Yo-Yo from the future, one who has lived through the time loop and endured endless torture. She reveals that the team's ultimate return will bring the end of the world and that the only solution is to let Coulson succumb to his infection. As Flint recreates the monolith, Mack leaves to find Yo-Yo and witnesses her future self's death by Kasius, who consumes the remaining odium and fights him. With help from Simmons, Mack kills Kasius and reunites with Yo-Yo, who is still alive in their timeline. Deke returns to the Zephyr in time to save Enoch and fix the machine, although seemingly at the cost of both of their lives, as the team returns to the present.

Back in their time, the team meets Noah, Enoch's successor, who has been monitoring the world from the Lighthouse in their absence. Coulson, May, Fitz, Simmons, Mack, and Yo-Yo investigate a beacon emitting from Earth, which fits Voss' description of the first signs of the end. Reluctant to join the team, Johnson stays behind and discovers that Deke survived the explosion. After he is arrested, Johnson is forced to leave the bunker to save him and prevent him from exposing the team, who are now most wanted. Upon finding the beacon, the team reunites with Agent Piper, who is revealed to be working for General Hale. They are then ambushed by a group of Hale's robotic soldiers, led by an assassin. During the fight, the assassin attempts to kill Mack with their chakram, but Yo-Yo blocks the attack and loses both her arms. Piper realigns with the team as they retreat to the Lighthouse with the beacon, which detonates as Noah sacrifices himself to save Johnson and Fitz. Later, General Hale criticizes the assassin, revealed to be her daughter, Ruby, for jeopardizing the operation. In Philadelphia, General Hale recruits Carl Creel to join her team, to which he reluctantly agrees.

The destruction of three monoliths caused by the beacon's explosion creates a dimensional rift that manifests the fears of the team. Using gravitonium, Fitz creates a device capable of sealing the rift; Coulson volunteers to deliver the device before he collapses. The team finds out about his infection, which is a result of the Ghost Rider burning off the life-sustaining GH.325 drug within him. The team is forced to accelerate their plan when Yo-Yo is attacked by a manifestation of a Simmons LMD. Coulson sends Deke to the surface to call for backup, then proceeds alone to seal the rift. He encounters a manifestation of Mike Peterson, who claims that Coulson's experiences are just a dream, and that he is dying on an operating table after the Battle of New York. Coulson overcomes his fear, and is saved by the real Peterson, who responds to Deke's call and arrives with several other S.H.I.E.L.D. agents. Coulson and Peterson fight off manifestations of Vrellnexians, Lash, and Hive, before managing to contain the rift. Later, the team organize a wedding ceremony for Fitz and Simmons. General Hale, who is investigating sightings of Johnson, finds evidence that Deke is related to Fitz and Simmons.

When the rift begins to reopen, Fitz sends the team to search for more gravitonium. The team hunt down a lead in Baton Rouge; Mack reunites with his school mate, Tony Caine, who has been helping to redeem scientists coerced into working for Hydra through Cybertek Industries. Caine states that the gravitonium was in transport aboard the Principia, a Cybertek ship that went missing. Deke realizes the gravitonium may have been activated by the lightning storm, sending the Principia into the sky. Following Deke's theory, the team find the Principia suspended in the atmosphere and discover most of the gravitonium is gone, leaving only a small portion to sustain the ship. As Mack collects the remaining gravitonium, a group of Hale's robotic soldiers ambush them. The team successfully escapes the ship before it plummets back to Earth. Upon hearing his mother's saying in an exchange between Simmons and Yo-Yo, Deke realizes Fitz and Simmons are his grandparents. Meanwhile, General Hale continues to form her team by attempting to recruit Werner von Strucker, whose memory had been enhanced after S.H.I.E.L.D. revived him from a vegetative state. While Strucker initially rejects Hale's offer, Ruby convinces him to stay.

When Simmons is attacked by a manifestation of an astronaut, Fitz accelerates work on sealing the rift but struggles to figure out how to compress the gravitonium. Under stress, Fitz encounters his Framework alter ego, The Doctor, who taunts him. On the Zephyr, Coulson, May, and Agent Piper capture General Hale; however, she reveals she was prepared for such an occasion, and threatens to detonate explosives strapped to Creel if S.H.I.E.L.D. fails to comply. Anton Ivanov arrives, and Coulson agrees to accompany them despite May's unease. Simmons, Mack, and Yo-Yo are attacked by one of the robots that Mack brought back from the Principia. While dealing with technical malfunctions, Johnson is rendered unconscious by another robot and awakens restrained by The Doctor. Simmons finds Fitz trying to remove Johnson's inhibitor. She deduces that The Doctor was not a result of the fear dimension, but a projection of Fitz's internal turmoil. He reprogrammed the robots to isolate Johnson, whose powers he uses to compress the gravitonium and seal the rift completely. Deke attempts to comfort Simmons, while also revealing himself as their grandson. Later, Hale speaks to her mysterious benefactor, Qovas, who hands her a vial of odium and reminds her of her Hydra allegiance.

28 years ago, a young Hale was assigned by Daniel Whitehall to infiltrate the U.S. Air Force, and also to be impregnated via in vitro fertilization with Ruby as Hydra's next leader. In the present, Hale fails to convince a recently-awakened Talbot to release Hydra contraband. She also informs Coulson that an alien alliance known as the Confederacy had made contact with Hydra and offered to assist Earth in an impending invasion; she intends to betray the alliance by using Whitehall's particle-infusion chamber and gravitonium to create a Destroyer of Worlds. Though she intends for it to be Ruby, she suggests Johnson may be a better fit. Upon hearing this, Coulson denies her offer and reveals his trip to the future, but she doesn't believe him. Back at the Lighthouse, May and Johnson struggle to deduce Hale's motivations and locate Coulson. Johnson, who has been left as the de facto head of S.H.I.E.L.D., refuses to trust Fitz and goes in search of Robin. Simmons tells Fitz about their relation to Deke, suggesting they will survive despite the odds.

Under Hale's orders, Creel attempts to absorb the gravitonium and begins to see flashes of Franklin Hall. In anguish from his exposure to the gravitonium, Creel works with Coulson and Talbot to escape. Hale sends Ruby after them as Creel stays behind, allowing Coulson and Talbot to escape via the Confederacy's teleportation device. Meanwhile, Johnson and May locate Robin, who has stopped drawing her visions for some time after seeing her own death in the future. Upon seeing May, Robin begins to draw again, this time showing Coulson and Talbot's location in the mountains. Back at the Lighthouse, Simmons convinces Yo-Yo to help her free Fitz and pursue possible leads on Hydra's gravitonium-powered weapon. Together, they trick Mack into releasing Fitz, before locking him up. A flashback to four years ago reveals that Ian Quinn was tricked by Raina into being absorbed by the gravitonium.

Ruby pursues Coulson and Talbot at the mountains, but Johnson arrives in time to save them. Deke, in an attempt to cover for Johnson, is shot by Hale and her men, forcing S.H.I.E.L.D. to retreat. Deke is taken back to the Lighthouse, where Mack and Piper operate on him and successfully save him. May confronts Coulson about his recent actions, and eventually admits her feelings for him. Ruby, furious about her mother's attitude, decides to rebel and lock Hale in her cell, while she takes over and works with Strucker. Fitz, Simmons, and Yo-Yo travel to a Hydra facility in England, where they find the particle infusion chamber. Fitz damages one of the components to render it useless, but they are then surrounded by the robot soldiers. Yo-Yo attempts to escape and call for backup, but is forced to fight Ivanov. As she emerges victorious, she learns that Ivanov's body is linked to all the robots, thus is able to disable them altogether. However, Ruby and Strucker arrive and decide to capture Fitz and Simmons in order to have them repair the infusion chamber. Meanwhile, Johnson helps Talbot contact his family, but unknowingly helps activate his brainwashing through his wife, who has been compromised by Hydra.

After locating Blue Raven Ridge, Johnson and May are sent to apprehend Hale, who willingly surrenders after Creel informs her of Quinn and Hall's consciousnesses within the gravitonium. She reveals that Ruby plans to become the Destroyer of Worlds and takes them to her. They arrive at the site, just as Ruby begins the infusion process, but Strucker is forced to stop the process at 8%. Unable to control the element, Ruby inadvertently crushes Strucker's skull, killing him. While May extracts Fitz and Simmons, Johnson and Hale attempt to calm Ruby down. Yo-Yo returns for Johnson, though upon realizing Ruby is the Destroyer of Worlds and the one who cut her arms off, she slices Ruby's neck with her own chakram in retaliation. Ruby's body releases a blast of energy as Hale escapes. Back at the Lighthouse, Talbot attempts to kidnap Robin, but Coulson and Mack manage to subdue him. Later, Hale is seen in the Confederacy ship, where she reveals S.H.I.E.L.D.'s possession of the gravitonium to Qovas.

Coulson puts the base on lockdown as Qovas and his Confederacy ship appear above River's End. Despite this, Qovas' troops, the Remorath scavengers, are able to teleport inside in pursuit of the gravitonium. While Coulson, May, Mack, Fitz, and Deke defend the control room, Yo-Yo retrieves Talbot and proceeds to the lab where Simmons, Piper, and Davis are guarding the gravitonium. Yo-Yo, Piper, and Davis attempt to clear the halls, when Talbot ices Simmons and places himself in the particle infusion chamber, absorbing the remaining gravitonium. With his new powers, he is able to rescue the S.H.I.E.L.D. agents, before taking off with Coulson to an unknown location. Meanwhile, Johnson relocates Robin and Polly with the help of Caine, who also gives her the Centipede serum, which was once used to keep John Garrett alive. However, Caine fails to retrieve a special ingredient, prompting Johnson to dig up her mother's grave.

After arriving on Qovas' ship, Talbot assumes leadership and demands an audience with the Confederacy. To prove himself, Talbot expresses control over his new abilities by killing one of the leaders and taking his place in the alliance. Kasius' father, Taryan, attempts to manipulate Talbot into increasing his powers by revealing untapped subterranean deposits of gravitonium on Earth, which would allow him to save the world from Thanos' imminent invasion. Coulson and Hale fail to convince him of Taryan's true motives and are forced to comply. Back at the Lighthouse, an odium-powered Remorath warrior attacks Mack before succumbing to the substance. As Simmons studies the odium, Johnson returns with Jiaying's corpse and the Centipede serum, tasking her to find a cure to save Coulson. Meanwhile, the team equip the Zephyr with gravitonium for space travel and proceed to Qovas' ship. Johnson and May infiltrate the ship, but are forced to surrender when Talbot incapacitates Johnson. Talbot kills Hale after she attempts to trigger Talbot's brainwashing. Later, Johnson is imprisoned and awakens to Taryan, who plans to take her back to his homeworld.

As an unconscious Johnson is being transported, Taryan communicates with her using a device. Johnson destroys the device and awakens, then evades her captors. After Talbot leaves on a Quinjet for Earth, Deke rescues Coulson and May, then reunites with Johnson. At a hospital, Talbot approaches Creel and offers him peace by turning him into gravitonium; he then absorbs Creel. Deducing Talbot's desire to prove himself a good father, Mack and Yo-Yo track him to his family's home. Talbot threatens the agents; his son George dissuades him from causing further harm, and he leaves to prove his heroism. Meanwhile, Coulson leaves with Johnson on the Zephyr, while May duels with Qovas as Deke redirects the missiles to target the ship itself. May and Deke successfully teleport back to Earth as Qovas perishes along with the ship. On the Zephyr, Coulson is attacked by a Remorath, and begins to bleed out as his condition worsens. At the Lighthouse, Fitz and Simmons explain that the remaining Centipede serum could be combined with Jiaying's DNA or odium, which would respectively allow the team to save Coulson or stop Talbot. Elsewhere, Talbot captures Polly and Robin, and asks the latter for the gravitonium's location.

The team argues about the usage of the Centipede serum until May destroys the odium vial. Deke advises Johnson to help unite the team and settle their differences. Under coercion, Robin informs Talbot of a gravitonium deposit in Chicago, to which he commandeers Qovas' ship. Johnson chooses Mack to lead S.H.I.E.L.D., and he coordinates the team as they evacuate as many civilians as possible. Simmons provides Coulson with the Centipede serum, but he refuses to take it and discreetly hides it in Johnson's gauntlets, and convinces her to face Talbot alone. Johnson attempts to appeal to Talbot's patriotism, but Talbot attacks and attempts to absorb her. Discovering the serum, Johnson injects herself with it and uses her enhanced abilities to blast Talbot into space, thus changing the timeline. While rescuing Polly and Robin from Qovas' ship, Fitz is mortally wounded by falling debris, and May and Mack stay by his side as he dies. Simmons resolves to find the present version of Fitz who is in stasis aboard Enoch's ship. After bidding his fellow agents farewell, Coulson is accompanied by May as he leaves S.H.I.E.L.D. to spend his last days in Tahiti.

A year after the death of director Phil Coulson, S.H.I.E.L.D. is rebuilding under the leadership of Alphonso "Mack" Mackenzie. They investigate a series of energy anomalies formed by hostile strangers emerging from portals, one of whom gets trapped inside a wall and partially turns to concrete. In deep space, Agents Daisy Johnson, Jemma Simmons, Piper, and Davis search for Leo Fitz, who was last seen in a cryofreeze chamber on a spaceship with the Chronicom Enoch; they find the spaceship abandoned and the chamber empty. Simmons learns that the chamber was created on Naro-Atzia, but the others decide to return to Earth. They are attacked by a Confederacy cruiser and, in the rush to escape, Simmons plots a course to Naro-Atzia. Mack and Melinda May recruit Dr. Marcus Benson to help found a S.H.I.E.L.D. academy and provide science support. They find coordinates on the man in concrete, Tinker, which lead them to a museum. The surviving hostiles are there and destroy the building to make way for their leader, Sarge, who looks just like Coulson.

Sarge and his crew begin to gather supplies for their mission, hiding their truck using cloaking technology. They rob a jewelry store to gather piezoelectric gems, attracting the attention of S.H.I.E.L.D. May and Elena "Yo-Yo" Rodriguez lead a team to capture Sarge and his crew, but are locked out of the vault. On a hunch, May finds the hidden truck where Sarge's crew is using a portal to move the gems out of the vault. May overpowers Jaco, Snowflake, and Pax, but hesitates when she sees Sarge. Sarge's team pushes May through the portal before closing it. Investigating Tinker, Benson decrypts a memory chip on him and finds footage of Sarge and his crew witnessing the destruction of a planet. In space, Fitz is out of cryo and hiding on a cargo ship with Enoch. They are discovered by the ship's controller, Viro, who threatens to kill them unless they work as slaves. Fitz tricks Viro into being sucked out of an airlock and changes course to Kitson, where the ship's crew can find new work. They had been nearing Naro-Atzia, Daisy's group's destination after their Confederacy run-in.

Fitz and Enoch arrive on Kitson, but their ship gets stolen at gunpoint, so they decide to head to the local casino to win enough money for a new ship in spite of their strict rule against "robots." Meanwhile, Daisy's group arrives on Naro-Atzia, where they are boarded by Malachi, a bounty hunter looking for Fitz. They manage to tie him up and find out that Fitz headed to Kitson, where they arrive later. Meanwhile, Enoch wins multiple consecutive games, but gets played and loses all their winnings. Needing to win a large sum and lacking money to bet, Fitz enters a game where he is himself the collateral: losers are sold into slavery. Daisy, Simmons, and Davis eat some alien "puffs," only to learn the hard way that they are hallucinogenic. The bounty hunter, revealed to be another Chronicom, knocks out Davis and overrides Enoch's systems remotely, revealing Enoch as a "robot" to the casino runners. Despite being high, Daisy is able to defeat the Chronicom hunter's gang. Simmons momentarily reunites with Fitz before the bounty hunter himself teleports away with him, leaving her and Enoch baffled. Meanwhile, back on Earth, Sarge shoots statically-charged particles into the atmosphere, covering the entire planet.

Deke Shaw is revealed to have started a company using S.H.I.E.L.D.'s tech. Sarge and his team track down a seemingly normal man and kill him with a strange knife. The body is brought to Benson, who discovers a bat-like alien parasite that revives and flies into the vent system after the knife is removed. Sarge's team goes after Shaw as their next target, with Sarge himself pretending to be Coulson to get close to Shaw. Eventually, he realizes it's not Coulson and attempts to escape, aided by an undercover S.H.I.E.L.D. agent assigned to keep an eye on him. Mack, May, and a strike team enter the building and attempt to apprehend Sarge and his team alive. Though Mack is able to capture Pax and Jaco while May defeats Snowflake, Sarge gets the upper hand and kidnaps May. While tracking the parasite, it flies into Agent Keller's mouth and starts fusing with his vascular system. Benson and Yo-Yo attempt to get him to a containment room, but he explodes in a mass of crystalline structures. Yo-Yo retrieves the knife and stops the parasite from destroying the base, but is left devastated by her failure to save Keller.

While in Sarge's custody, May is forced to kill a parasite-infected man. Afterwards, he reveals that it was part of the "Shrike," parasites that infect worlds and destroy them on behalf of their creator, and that he intends to stop them once and for all. May's eventually able to turn the tables on Sarge and brings him back to base, all while experiencing memories of Coulson. Daisy's team is captured by Chronicoms led by Atarah, Enoch's former superior. After their homeworld was destroyed by a mysterious plague, they took the Confederacy's ships to defend themselves and kidnapped Fitz to unlock the secret to time travel. With Enoch betraying them and no other choice left, Simmons surrenders to the Chronicoms in order to reunite with Fitz so Daisy and her team can live and return to Earth. Mack and Benson comfort Yo-Yo, who's still affected by Keller's death. While performing the autopsy, Benson learns that the parasite and the knife used to kill it were composed of crystals similar to the Monoliths the S.H.I.E.L.D. agents have encountered in the past. Enoch reunites with Fitz and gets him up to speed on what's happened before gassing him, betraying him as well.

Atarah uses a special device to trap Fitz and Simmons inside their own minds, forcing them to work together to figure out time travel logic. While imprisoned, Fitz learns from a reluctant Simmons of her time-traveling adventures, including the deaths of his alternate future self and Coulson. The two of them are then pursued by Fitz's Framework persona as well as an undead Simmons, formed from her suppressed pain and bad memories from throughout her life. After a brief argument, Fitz and Simmons reconcile and overcome their fears. They are then freed by Enoch, who has had second thoughts about his allegiances and manages to overpower Atarah and the other Chronicoms. The three of them then teleport away to an unknown destination. Back on Earth, Daisy briefs Mack on Fitz and Simmons' situation and learns that Earth is being invaded by the same creatures that are responsible for the Chronicom homeworld's destruction.

Fitz, Simmons, and Enoch end up teleporting back to Kitson, where they are captured by Mr. Kitson, the planet's owner, and forced to gamble for their lives. However, a mysterious mercenary named Izel intervenes and buys their freedom in exchange for their help in finding an artifact on Earth. As they prepare a ship for departure, Enoch parts way with them, as he has now completed his initial mission, and sets out to help his people once more. Back on Earth, S.H.I.E.L.D. attempts to interrogate Sarge and his crew, but to no avail. Using one of his tracker devices, the team locates two Shrike hosts and captures them. However, both hosts cause a violent interaction when in close proximity, creating another crystallized explosion. Sarge reveals their weakness against cold exposure, which helps save May and Yo-Yo in time, in exchange for his and his crew's freedom.

Sarge reveals that a large number of Shrike hosts will converge at a specific site to create a crystallized tower in preparation for the arrival of "the Beast." Mack assigns Daisy, May, and Deke to accompany Sarge and Snowflake to the site while he secretly follows them on the Zephyr. While being imprisoned onboard, Pax reveals to Yo-Yo that Sarge's plan is to use a bomb to detonate the tower and take out the Beast, who Sarge reveals to be Izel. As they head back toward Earth, Fitz and Simmons learn from Izel that she is looking for the monoliths, known as the Di'Allas. Izel secretly begins using Shrike to infect the ship's crew one by one until only Fitz and Simmons are left. As Daisy, May, and Deke find the bomb, Sarge teleports back to the Zephyr after setting the truck to collide with the tower. Back on Kitson, Enoch establishes contact with one of his associates, Isaiah, and proposes an alliance. Meanwhile, the Chronicom hunters attempt to take down Enoch by using their memory machine to learn from Fitz and Simmons' memories.

Sarge takes over the Zephyr and commands Mack to pursue Izel's ship. Deke fails to disarm the bomb, but as the truck collides with the tower, Daisy uses her powers to contain it, preventing it from exploding. The collision releases a swarm of Shrike that surround the truck, but Daisy is able to quake them apart. Izel commands the spaceship to retreat. Sarge kills Pax in anger after learning the bomb plot failed. When Fitz and Simmons successfully make contact with S.H.I.E.L.D., Sarge threatens Izel. Believing Fitz and Simmons to be conspiring against her, she commands the ship's crew to eliminate them. Yo-Yo convinces Jaco to remember his purpose for fighting, leading him to help them. Mack frees himself with Yo-Yo's help and overpowers Sarge. Mack, Yo-Yo, Davis, and Jaco then infiltrate Izel's ship and rescue Fitz and Simmons, but Izel disappears. The group escapes the ship through the portal into the truck, reuniting with Daisy and the others. Jaco decides to go back and detonate the bomb, sacrificing himself in the process. Later, S.H.I.E.L.D. celebrates their victory while Sarge is imprisoned. Mack and Yo-Yo reconcile and rekindle their relationship. Later, May enters Sarge's cell and seemingly kills him.

Sarge's body is taken to the lab, where Fitz and Simmons learn that he is still alive and that his wounds are healing fast. May submits to capture and confesses. However, she later claims that she doesn't remember. Eventually, the team deduces that Izel has the power to possess people and that she infiltrated the Lighthouse through Davis. Mack puts the base on lockdown and gathers everyone at the command center for questioning. After Mack locks up Daisy and Yo-Yo to prevent them from being controlled, Izel appears and demands the Monoliths. The agents attempt to stop her, but Izel keeps hopping through them until she drops Davis from a ledge, killing him before taking Mack. Fitz deduces that the Monoliths represented space, time, and creation. When they exploded, their combined energy created a new Coulson and sent him to another planet in the past. Sarge escapes and confronts Izel, who's found the device containing the Monoliths' energy. She reveals that his real name is Pachakutiq, they're both from a planet of non-corporeal beings, and he had gotten his memories confused with Coulson's when he took the Coulson body. Despite this, Sarge refuses to join Izel. When Yo-Yo and Daisy confront her, the former allows herself to be possessed and demands Mack fly her somewhere else. Shaken, Sarge refuses to believe Izel, even as his powers start to manifest.

Izel plans to take the Monolith energy to a specific temple, so she possesses Mack and summons Benson. Though Yo-Yo successfully warns him before he reveals the information, Izel torments Benson with a manifestation of his deceased husband, Thomas, until he gives up the location. Yo-Yo and Mack trick Izel into releasing Benson so he can let S.H.I.E.L.D. know where she is headed. Daisy and May argue over whether any trace of Coulson lies inside Sarge and if they should further antagonize him to unleash his power against Izel. Deke realizes Izel's ability is based on vibrations, so he, Fitz, and Simmons begin working on a device to counter it. Daisy finally reads the letter Coulson left for her and snaps Sarge's neck. Sarge comes back stronger and begins destroying the Lighthouse, trying to escape. As Daisy prepares to kill him, he calls her "Skye." Daisy realizes Coulson really is in there, so she calms him down and sees him as an ally. Imprisoned in the temple, Izel demands Mack and Yo-Yo recreate the Monoliths' solid forms. They refuse, but are shocked when Flint suddenly appears. Meanwhile, the Chronicoms have learned new information. While Atarah still wishes to save Chronyca-2, Malachi wishes to establish a Chronyca-3, so he kills Atarah and sends other Chronicoms after two targets.

possesses Flint to rebuild the Monoliths, creating a portal where her people await a sign to invade Earth before breaking Flint's leg and sending out a Shrike army for more hosts. Deke brings his tech company staff to the Lighthouse to mass-produce the devices needed to counter Izel and turn Sarge's daggers into Shrike-killing bullets. May, Sarge, Piper, and Daisy take a Quinjet to the temple. Daisy leads the Shrike-infected zombies away while May and Sarge go to confront Izel. Fed up that nobody respects him, Deke uses his stolen jump-drive to go to the temple himself and free Mack, Yo-Yo, and Flint. Despite not having enough power for a return trip, he manages to set up a camera to show Fitz and Simmons what Izel is doing and make it to the Quinjet on foot. Mack and Yo-Yo have Piper fly Flint to safety, but zombies trap them and Daisy in the Zephyr. Sarge and May face Izel, but Sarge cannot kill her. Confused about the pain he is in, May tells Sarge it's love for the team, but he stabs her and sends her through the portal as the sign, embracing Pachakutiq. Meanwhile, Enoch meets with his contact on Kitson, who tells him all the Chronicoms are now hunters and attacks him.

Fitz and Simmons tell the field team what happened to May, but communications are shut off and the Lighthouse is put on lockdown. Malachi and the Chronicoms attack, using Fitz and Simmons' knowledge to anticipate their every move. Barricaded in a room with Framework tech, Fitz and Simmons prepare to sacrifice themselves to destroy it so the Chronicoms can't use it, but a disguised Enoch saves them and proposes a plan. With the Zephyr disabled, Mack has Deke fly the Quinjet to them, but Yo-Yo is infected by a Shrike. In between realms, where life and death don't matter, May destroys three hooded figures before they can let Izel's kind through. Izel herself appears and overpowers her to establish the connection. Daisy, Mack, and Yo-Yo battle Pachakutiq, but are no match for him. Izel reappears, but May stabs her from behind, killing her and freeing Yo-Yo. Mack kills Pachakutiq, closing the portal. As May slowly dies, Simmons appears with a team and an upgraded Zephyr, putting May in a stasis pod. Everyone evacuates before the Chronicoms destroy the temple and Monoliths. Fitz remotely sends them to safety with an upgraded jump-drive, landing them several decades in the past above Manhattan. Simmons explains that the Chronicoms know everything about S.H.I.E.L.D. and that they need an expert to help them fight back, revealing a Chronicom tech-enhanced Coulson LMD.

In 1931 New York City, several Chronicoms steal the faces of three police officers and kill a contact from a local speakeasy. S.H.I.E.L.D. agent Jemma Simmons introduces Director Alphonso "Mack" Mackenzie and agent Daisy Johnson to an LMD version of Phil Coulson, who struggles with his existence and the amount of information uploaded into him. Daisy and Deke Shaw investigate the faceless officers and are attacked by the Chronicoms, but they overpower one and take him back to the Zephyr. Coulson and Mack investigate the speakeasy and meet its owner, Ernest "Hazard" Koenig, who reveals that the police officers are providing security for a function in honor of Gov. Franklin D. Roosevelt. Simmons overloads the Chronicom's mind, forcing it to reveal their actual target: Koenig's employee Wilfred "Freddy" Malick, father of future Hydra leader Gideon Malick. The team rescues Freddy from the Chronicoms and realize they have to save Hydra to ensure S.H.I.E.L.D.'s future. On the Zephyr, the Chronicom Enoch, an ally of S.H.I.E.L.D., helps heal Agent Melinda May.

Deke and Mack promise to keep Freddy safe, traveling with him by train to make a delivery. The other agents regroup at Koenig's speakeasy and interrogate Freddy's contact, Viola; learning she is a Hydra agent and that Freddy is carrying what will become Hydra's super soldier serum. They return to the Zephyr, where Enoch attempts to prevent an erratic May from leaving the ship. Coulson stops her, but she reacts apathetically to his presence. Koenig helps direct the team to Freddy's delivery location, learning of S.H.I.E.L.D., Chronicoms, and time travel in the process. Daisy contacts Deke and tells him to kill Freddy to stop Hydra's rise, but Mack prevents this. Koenig tries to stop Freddy from making the delivery, but Freddy shoots him and leaves with a Hydra agent, securing their future. The Zephyr unexpectedly time travels to follow the Chronicoms through the next time window, leaving Enoch behind. Despite this, he is hired by the recovering Koenig and agrees to tell him more about S.H.I.E.L.D. and robotics.

The agents end up in 1955 near Area 51, a S.H.I.E.L.D. base currently working on Project Helius, an ion fusion reactor prototype. The agents kidnap high ranking agent Gerald Sharpe and have Coulson impersonate him while Simmons impersonates Peggy Carter so they can find the Chronicom infiltrators. However, they run into Carter's former partner Daniel Sousa, who outs them. Despite putting up resistance and his racism towards part of the team, Sharpe eventually reveals that Helius cannot function without a powerful energy source, leading Deke to deduce that the Chronicoms plan to sacrifice one of their own to activate the weapon and destroy the base. Daisy arrives undercover and convinces Sousa to release her teammates just as the undercover Chronicoms enact their plan. Daisy and Simmons improve a S.H.I.E.L.D. EMP device in time to disable Helius, along with the entire base, the Chronicoms, and Coulson. Mack and Deke return Sharpe to the desert and pose as aliens to avoid changing history.

Coulson wakes up in Sousa's custody with a system glitch that makes him see in black and white and hear an internal monologue (in the style of a film noir). He realizes that the current date is the day Sousa dies while delivering a device to Howard Stark. Coulson calls the Zephyr with the help of Enoch at the speakeasy. Elena "Yo-Yo" Rodriguez and Deke find the device, but the latter is captured by Hydra. He is taken to an older Wilfred Malick, who spares Deke's life since Deke spared his in 1931. Yo-Yo and Simmons discover that May experiences other people's emotions. Mack, Coulson, and Daisy realize that Sousa is killed by Hydra to prevent him from exposing their presence within S.H.I.E.L.D. They decide to change history and save Sousa; after he delivers the device, Coulson knocks Sousa unconscious and fakes his death. Sousa wakes up on the Zephyr and a repaired Coulson explains their situation. They travel forward in time again, while a Chronicom stays behind in 1955 and offers to help Malick.

In 1973, the agents return to the speakeasy to discover that S.H.I.E.L.D. is preparing Project Insight, which should not be developed for several more decades, led by Wilfred Malick, who should have died in 1970. Wilfred and the Chronicoms attempt to capture the agents, but Daisy briefly takes his son Nathaniel (who also should be dead) hostage to allow their escape. Nathaniel sees Daisy use her powers. The agents reunite with Enoch and return to the Zephyr. Without warning, the Chronicoms jump forward to 1976 when Project Insight is set to launch, and the Zephyr follows. Coulson and May plant explosives in the Lighthouse where Insight is being launched while Deke and Yo-Yo confront Wilfred, who is killed by Deke. Daisy and Sousa are captured by Nathaniel. Mack aborts the detonation when he sees his parents, John and Lilla, are being held captive, allowing Insight to launch. The agents use the Zephyr to destroy Insight, giving away their location. Nathaniel attempts to call Daniel Whitehall to transfer Daisy's powers to himself.

The Lighthouse automatically fires missiles at the Zephyr, damaging the time drive. While Deke, Simmons, and Enoch repair it, Deke discovers that Simmons has a memory implant that blocks her knowledge of Leo Fitz's location while retaining information on time travel. Nathaniel experiments on Daisy and transfers her powers to himself, but he is overwhelmed by them as they destroy the building he is in, allowing Sousa to get Daisy back to the Zephyr. May uses her powers to identify undercover Chronicoms while she and Coulson rescue General Rick Stoner, and Coulson finds the Chronicoms' ship. He speaks with their predictor, Sibyl, before blowing up the ship with himself and many of the Chronicoms in it. Mack and Yo-Yo discover that Mack's parents are already dead and being impersonated by Chronicoms, forcing Mack to throw them from the Quinjet. The Zephyr jumps to 1982, and Mack steps out to mourn. Deke checks on him, but they are stranded when the Zephyr suddenly jumps through time.

Stuck in 1982, a despondent Mack spends the next year alone in grief. Deke checks in on Mack occasionally, and eventually convinces him to come see Deke's new band, The Deke Squad, which include Olga Pachinko, Roxy Glass, Cricket and twins Ronnie and Tommy Chang, which performs 80s' classics that have not been written yet. Deke reveals that he has secretly been training the members of the band to be S.H.I.E.L.D. agents, and that Coulson's consciousness has been saved on a hard drive. Meanwhile, Sibyl's consciousness also survived, and she uses a lonely programmer to construct a crude body for herself. She then creates new "hunter" robots that kill the programmer before invading the Lighthouse in search of the time stream that Sibyl uses to predict the future. Mack helps Deke and the new agents defeat the hunters, unaware that a small robot escaped with the time stream. The Zephyr re-appears long enough for May and Yo-Yo to reunite with Mack and Deke. The latter recounts the past year's events to May. The small robot takes the time stream to Nathaniel, who survived the collapse and is now working with Sibyl.

After rescuing Mack, Deke, and Coulson, Simmons informs the team that the time drive keeps jumping them forward by less time until it will eventually collapse on them. Needing Yo-Yo's currently inactive powers to deactivate it, Daisy suggests stopping by Afterlife to get help from her mother Jiaying. Yo-Yo and May arrive to discover that Jiaying is in the process of helping a despondent Inhuman named Kora with her volatile energy powers. After examining Yo-Yo, Jiaying comes to the conclusion that her problems are mental rather than physical and has May use her empath abilities on her. Yo-Yo reveals that she witnessed the death of her uncle and has since blamed herself for it. Nathaniel arrives and recruits Kora in taking over Afterlife. Yo-Yo, May, Jiaying, and young Inhuman Gordon are forced to flee. Upon arriving back at the Zephyr, Yo-Yo realizes that she has been holding herself back and successfully deactivates the time drive. As the crew settles in, the time drive suddenly starts up, causing the Zephyr to unexpectedly jump again.

The Zephyr gets trapped in a time vortex as Daisy wakes up from her cryo-chamber. After witnessing several events happen, time suddenly restarts and she realizes that she is trapped in a time loop as the Zephyr gets closer to the center of the vortex with every passing loop. She learns that Coulson is also aware and has been in the loop longer, though Daisy forgets everything when she dies. Daisy and Coulson learn about Simmons' memory implant, but when they try to remove it, a freak accident kills her. The deaths appear to be orchestrated and Coulson concludes that Enoch, who was programmed to protect Simmons' implant, has been unwillingly killing them. After several failed attempts, they eventually manage to remove the implant and Simmons informs them that Enoch's power mechanism can fix the time drive, though at the cost of his life. In the final loop, Enoch willingly gives up his mechanism and dies, but not before revealing to Daisy that this will be their final mission as a team. Meanwhile, Nathaniel helps Kora control her powers.

Nathaniel recruits a young John Garrett, who turned against S.H.I.E.L.D. and was killed by Coulson in the original time. Nathaniel shows him this future while perfecting a way to transfer Inhuman powers to his men. S.H.I.E.L.D. keeps Jiaying at the Lighthouse for protection. Daisy learns that Kora is her half-sister, who died before Daisy was born in the original timeline. She spends time with Jiaying but does not tell her that she is her daughter. Coulson and Gordon teleport into Afterlife, but Nathaniel anticipates this and captures them. He transfers Gordon's powers to Garrett, killing the former in the process. Garrett teleports Nathaniel to the Lighthouse, while Yo-Yo and Mack rescue the captive Inhumans and Coulson. The latter takes Kora captive. Nathaniel reveals to Jiaying that Daisy is her daughter, before killing Jiaying and fleeing. Garrett kidnaps Simmons as he and Nathaniel steal the Zephyr, unaware that Deke is still aboard. Nathaniel explains his plan to have Simmons tell them where Fitz is, as he is the only one who can stop them.

Kora claims that she wants to work with S.H.I.E.L.D., despite the agents deducing that she has ulterior motives. Knowing that Sibyl is aware of their every move, Daisy, Sousa and Mack decide to act unpredictably and take a quinjet to follow Nathaniel and the Zephyr into space. Nathaniel attempts to glean information from Simmons by using Deke as leverage, but is unable to find Fitz's location in her memories. His actions cause Simmons to forget who Fitz is completely. May interrogates Kora, who shuts down the Lighthouse's power, allowing Sibyl to hack into the mainframe. Coulson realizes that he can read the computer code that she is using and tries to shut her out. Kora suggests using their future knowledge to go after those who deserve to be killed, but May shows her Jiaying's body and she lashes out, only to be teleported by Garrett back to the Zephyr. Daisy, Sousa, and Mack watch as a Chronicom fleet arrives to meet the Zephyr. The Chronicoms use the information that Sibyl stole to destroy S.H.I.E.L.D.'s facilities around the world.

Upon landing on the Chronicom ship, Daisy searches for Deke and Simmons while Sousa and Mack fend off a group of Chronicom soldiers. Sibyl plans for Daisy to find Simmons to jog her memory, but an impatient Nathaniel has Kora confront them. Daisy talks her down and let them escape, forcing Nathaniel to knock Kora out and have her powers transferred to him. The agents return to the Zephyr and escape the ship. With the Lighthouse the only S.H.I.E.L.D. base still standing, Garrett plants bombs to destroy it, but Coulson, Yo-Yo, and May capture him and neutralize his powers. When they force Garrett to stop the explosion, Nathaniel leaves Garrett to die, but they all manage to survive. Garrett decides to join the agents and teleport them to the speakeasy, only to be killed by other agents who arrived there to hide. Everyone regroups and, with Simmons' help, create a "key" that she was struggling to remember. The key opens a portal that brings Fitz to them, but he is disappointed to learn Simmons does not remember him.

Fitz explains that he has traveled from their original timeline to this new one using the Quantum Realm. Deke decides to remain in the new timeline to help send the others and the Chronicoms back to the original one, becoming the new leader of S.H.I.E.L.D. When they arrive back in the original timeline, Fitz helps Simmons remember him and the life they lived while they were building the time machine, including their daughter Alya. Coulson, May, Mack, and Daisy infiltrate the Chronicoms' ship to rescue Kora and confront Nathaniel. May and Kora combine their abilities to give empathy to the Chronicoms, ending their assault. Daisy fights Nathaniel before destroying the Chronicoms' ships, killing him and Sibyl. The agents find Daisy in space, and Kora revives her. One year later, Fitz and Simmons have retired to raise Alya; May is a professor at S.H.I.E.L.D.'s Coulson Academy; Mack continues to lead S.H.I.E.L.D., with Yo-Yo as one of his top agents; Daisy is exploring the cosmos with Sousa and Kora; and Coulson decides to travel the world.

Krista Starr returns home from Iraq, and it's not long before she finds out her twin brother Zack, has been killed. She hunts for the man that killed her brother. Blade is also hunting for the same man, which Krista and Blade team up to take down, but things don't turn out so good for Krista.

Krista wakes up to face the realities of her vampire state, and Marcus explains the rules pertaining to the Houses. Blade seeks out Rev. Carlyle to get a lead on the vampiric-ash trade, then uses Krista to get information on the super-vampire Fritz.

Blade and Shen track down a vampire name Sands, who was used in Marcus's experiments. Krista visits her mom for the first time after being turned, she also tries to get a sample of the vaccine and accompanies Chase to a AA meeting.

Blade is caught by a group of vampires called Bad Blood and Reverend Carlyle is in on it. Krista is heading to the House of Leichen, so she can have a vision to find Boone.

Krista hunts down Boone through their spirit connection, while Marcus sends Chase to Berlin to track down one of Dr. Vonner's pregnant patients - a woman whose child-to-be harbors a dark secret. Blade follows Chase to get the woman first, while Marcus reveals the secret of Aurora to Krista.

Krista gets some bad news about her mother. Marcus tries to find a way to get Vanessa back from Blade and sends Krista to Berlin to do so.

Blade tries to solve the murder of a cop named Flanigan who helped care for him while growing up. Flashback scenes tell how Blade's father brought in Abraham Whistler once he could no longer do anything about Blade's need to feed. Krista copes with her mother's critical condition.

Lisa Starr, now a vampire, is on the loose and it's up to Blade and Krista to find her and give her the serum. Chase gets in touch with a old flame named Alex, he wants her to leave Marcus.

After her mother's death, Krista becomes increasingly disconnected from both Marcus and Blade. Blade finds out about the liquid that was taken from Vanessa, while Damek makes his move on Marcus.

Blade and Shen learn that the White Prince, an infamous vampire and serial killer, has made a resurgence and is working out of a Detroit nightclub. Blade has Krista detox after she feeds off of Marcus. And Charlotte makes a deal with Chase.

Agent Ray Collins and Blade team up to take on the vampires. Marcus finally makes his move on the Purebloods by first going after Charlotte and then the Conclave.

Marcus makes the final move on the Purebloods and also discovers the whereabouts of Blade's and Shen's main hideout. This leads to a final showdown between Marcus and Blade as well as Krista and Chase!

Criminals, including the Russian mafia, Yakuza, and Chinese, have taken advantage of Hell's Kitchen's circumstances since "the incident". Blinded as a boy in an accident that gave him heightened senses, Matt Murdock begins fighting this rising criminal element by night as a costumed vigilante while opening a law firm with his friend, Foggy Nelson. Their first client is Karen Page, a secretary for construction company Union Allied, who has been framed for the murder of her co-worker, Daniel Fisher, after accidentally uncovering a pension embezzlement scheme. Murdock prevents Karen from being prosecuted and protects her from an assassin, before exposing the scandal through Ben Urich at The New York Bulletin. Grateful for their help, Page offers to work for Murdock and Nelson. James Wesley covers up the involvement of his employer in the scandal, and orders Anatoly and Vladamir Ranskahov, the Russians' leaders, to deal with Murdock ("the man in black"): they kidnap a young boy to lure him into a trap.

When Murdock was a boy, his father was murdered for winning a match he was told to throw. Now, after failing to rescue the kidnapped boy, a severely injured Murdock is found in a dumpster by nurse Claire Temple. Nelson meanwhile attempts to comfort Page following her recent traumatic experiences. Temple takes Murdock to her apartment, tends to his wounds, and removes his mask, discovering his blindness. He refuses to reveal his name, but does reveal his heightened senses when they alert him to a Russian who is searching the apartment building, giving Temple time to hide Murdock and convince the man that she knows nothing. Murdock realizes that the man did not believe her, and overpowers him, taking him to the roof. Murdock and Temple torture him into revealing the boy's location, before Murdock pushes him off the roof and into the same dumpster. He barely survives. Murdock enters the building where they are keeping the boy, defeats the guards, and rescues him.

Wesley, having become aware of Nelson and Murdock because of their involvement with Page during the Union Allied scandal, hires them to defend John Healy, an assassin. Though Nelson wishes not to get involved with an obvious criminal element, Murdock wishes to use the case to discover who Wesley's employer is, and so accepts Wesley's offer, which includes a substantial sum to ensure their silence. Page receives a similar offer from Union Allied, who do not want her to talk to anyone else about the scandal, and threaten to sue her for leaking company secrets to the press if she does not agree. Despite this, Page goes to Urich, whose editor Ellison is forcing him to write superfluous stories rather than the major crime breaks of his youth, and offers to tell him more about the Union Allied scandal. After successfully defending Healy, Murdock confronts him in costume and forces him to reveal Wesley's employer, Wilson Fisk. Healy then commits suicide rather than face the consequences of this.

Murdock is unable to find any record of Fisk, and so continues to interrogate criminals, searching for answers. Wesley informs the Ranskahovs of an offer Fisk has made to help with their operations, given their recent failures. Angered at this apparent slight, they attempt to stop the man in black once and for all by visiting in hospital the Russian whom Murdock threw from the roof. After the Russian tells them of Temple, they send men to kidnap her, but she manages to call Murdock in time to alert him of her kidnapping. The Russians attempt to torture Murdock's name out of Temple, but Murdock arrives and defeats the gangsters. Seeing the aftermath of this, the Ranskahovs decide to agree to Fisk's offer, with Anatoly going to tell Fisk personally, by barging into the restaurant where Fisk is having dinner with an art gallery curator named Vanessa Marianna. Fisk takes a confused Marianna home, and angered at this intrusion and embarrassment, Fisk beheads Anatoly and orders Wesley to send the body to Vladimir.

Fisk explains the situation to his allies, including Chinese leader Madame Gao, of whom he asks a special favor. Elena Cardenas, a renter of powerful businessman Armand Tulley, comes to Nelson and Murdock after Tulley, who wants to convert her apartment building, sends men to wreck her home. Nelson goes to Tulley's lawyers at Landman and Zack (where he and Murdock once interned), represented by Marci Stahl, Nelson's ex-girlfriend. She explains that Cardenas and her neighbors can either take a large settlement or be evicted. While looking for complaints against Tulley at the police station, Murdock realizes Detectives Carl Hoffman and Christian Blake are corrupt when he hears them kill a Russian. Murdock later incapacitates Blake and uses his cell phone to find Vladimir. Fisk pays Turk Barrett to reveal to Vladimir that Fisk killed Anatoly, and as they prepare for a war against Fisk, their forces are destroyed in a suicide attack by Gao's workers. Vladimir survives, but Murdock finds him, as they are surrounded by police.

Murdock takes out the police when they try to kill Vladimir on Fisk's orders, and he takes Vladimir to an abandoned warehouse, hoping for answers about Fisk, while Nelson and Cardenas are injured in the bombings. With Temple's help, Murdock cauterizes Vladimir's wounds, alerting a non-corrupt police officer to their presence. The officer calls in Murdock and Vladimir's location, and the warehouse is soon surrounded. Blake and Hoffman take control of the situation, and await Fisk's orders. Fisk talks to Murdock via police radio, telling him of his admiration for what Murdock is trying to do, even though it clashes with Fisk's own plans to save the city. Fisk then frames the vigilante by having a police sniper fire on other officers from the roof of the warehouse, including Blake, as Urich and the media look on. Vladimir, in return for Murdock avenging Anatoly's death, gives him information on Leland Owlsley – the accountant for all of Fisk's operations – before giving his life so that Murdock can escape.

Murdock tracks down Owlsley, but is distracted by the arrival of an elderly man: Murdock's mentor, Stick, who taught him to master his abilities as a child, but abandoned him when Murdock developed an attachment to him. Now, he enlists Murdock's help in destroying Black Sky, a weapon that the Japanese, led by Nobu, are bringing to New York. Stick agrees to refrain from killing, but breaks his promise when he kills Black Sky, who is actually a young boy. After fighting in Murdock's apartment, Murdock defeats Stick, who agrees to leave the city. Urich, having agreed to help Page expose the further scandal and corruption surrounding Hell's Kitchen and Union Allied, explains that they need proof before they can publish anything. While searching for a connection between Tulley's men and Union Allied, Page is confronted by them. Nelson helps her escape them, so she and Urich explain their investigation to him. Stick later converses with a heavily scarred man about Murdock's role in events to come.

Page and Nelson bring Murdock in on their plan, and he agrees as long as they stop putting themselves in harm's way, and use the legal system rather than underhanded tactics. Owlsley and Nobu, angry at being confronted by the vigilante and losing Black Sky, respectively, express their displeasure with Fisk, while he is also dealing with Blake, who wakes up in hospital. Fisk convinces Hoffman to kill Blake before he can speak out against Fisk, but Hoffman is incapacitated by Murdock, who gets information on Fisk from Blake before he dies. Gao visits Fisk, warning him that he will have to get everything under control if he does not want her, Nobu, and Owlsley to side-step him. An angry Fisk is later consoled by Marianna, and he tells her of how, as a child, he murdered his father when he was beating Fisk's mother. She convinces him to stand up and go public with his intentions to save the city. This negates all of Murdock's information from Blake, which Urich was going to publish.

In the wake of Fisk's public revelation, Murdock, Page, Nelson, and Urich begin searching for something from Fisk's past that they can use against him. Murdock visits Marianna at her art gallery, hoping to gain insight into Fisk by speaking with her, and encounters Fisk himself. Nobu demands a promised city block from Fisk, who agrees on the condition Nobu provide him with a "specialist" in return to deal with the vigilante. The block, which Fisk has bought from Tulley, is where Cardenas lives, and she is one of the few tenants who stands in the way of Fisk gifting it to Nobu. When Cardenas is killed by a junkie, Murdock realizes that Fisk is behind it, and tracks him to an abandoned warehouse, where he is confronted by the specialist: Nobu. Murdock eventually defeats Nobu, accidentally causing him to burn alive, but sustains serious injuries. Fisk then confronts Murdock, beating him nearly to death. Murdock barely escapes, only to collapse at his home in front of Nelson.

After Temple tends to Murdock's wounds, Nelson confronts him about his "blindness" and vigilante activities. Murdock explains that after experiencing the twisted morals of Landman and Zack, Murdock took it upon himself to confront a paedophilic and incestuous rapist with no legal evidence against him, but who Murdock had discovered through his heightened senses. Since then, he had been doing everything he could to make the city a better place whenever the law could not. Nelson, unable to look past Murdock's lies, leaves their firm. Urich, after the extension on his sick wife's hospital stay is denied and he is offered a better paying job as an editor rather than a reporter, decides to give up the investigation. Page, in an attempt to change his mind, takes him to a rest home she just discovered, where they meet Marlene Vistain, Fisk's mother, who tells them that Fisk killed his father. Fisk, meanwhile, is throwing a charity gala to publicly raise money for victims of the bombings. There, many of the guests, including Marianna, are poisoned.

Still recovering from his injuries, Murdock says goodbye to Temple, who is leaving for a time. Before she goes, Temple suggests that he get better protection if he is going to continue his crusade. With the help of Barrett, Murdock finds Melvin Potter, a mentally unbalanced engineer who has been coerced into creating armored clothing for Fisk, and asks him to make a suit of body armor in exchange for stopping Fisk from hurting anyone else. Page wishes to reveal the story of how Vistain is alive, and says that Fisk killed his father, but Urich explains that it is unreliable, given her state of mind. While Fisk will not leave Marianna's side as she recovers in hospital, Wesley receives a phone call from Vistain and learns that Page and Urich visited her. He confronts Page and attempts to blackmail her into not exposing Fisk, threatening to hurt her friends. When Fisk calls Wesley to find out where he is, the ringing distracts him long enough for Page to take his gun, and kill him.

Using information from Urich, Murdock finds the base of Gao's heroin operation and dismantles it, with Gao, who can hold her own against Murdock, escaping and deciding to return to her homeland to think about the future. Fisk's men find Wesley, and the grieving Fisk realizes that the last person he talked to was Vistain. Wanting to keep those he loves safe by sending them out of the country, Fisk is unable to convince Marianna to leave him, but does get Vistain away, with the sick Vistain unable to tell him what her call to Wesley was about. Nelson continues his work without Murdock, and takes what they know to Stahl. Page, struggling to get over killing Wesley, convinces Urich to write the story, but it is rejected by Ellison. When Urich accuses Ellison of being paid off by Fisk, he gets fired. Urich decides to start his own blog to get Fisk's story out there, but Fisk's actual informant in the Bulletin tells him that Urich visited Vistain, angering him to the point that he breaks into Urich's apartment and kills him.

Murdock and Page attend Urich's funeral, while Fisk learns that Owlsley and Gao conspired to poison Marianna, whom they deemed a distraction, and that Owlsley has been hiding Hoffman as an insurance policy. When Owlsley tries to blackmail him, an infuriated Fisk kills Owlsley by throwing him into an open elevator shaft. Murdock and Nelson reconcile their differences, and begin building their case against Fisk. As the vigilante, Murdock finds Hoffman with information from Stahl and convinces him to testify against Fisk. Acting on this testimony, federal agents arrest Fisk and his co-conspirators, but Fisk manages to escape custody. Before he can flee the city, Murdock intercepts him, wearing the new armor made for him by Potter. After a brutal fight, Murdock defeats Fisk and leaves him to the police. With Fisk arrested, Marianna leaves the city. Murdock, Page, and Nelson celebrate their success and resume their work. The vigilante is named "Daredevil" by the media.

Following the downfall of Wilson Fisk and the Russian mafia, and the disappearance of the Chinese and Yakuza, various gangs attempt to take control of Hell's Kitchen, including the Irish Mob and Cartels. When a group of Irish are gunned down by an apparent "army", the sole survivor, Elliot "Grotto" Grote, seeks out the firm of Nelson and Murdock for protection. Karen Page, Nelson and Murdock's assistant—who is struggling to manage their financial troubles given that the firm's clientele often cannot afford legal fees—takes the wounded Grotto to the hospital, while Foggy Nelson learns from the Dogs of Hell biker gang that a group of their own was murdered by the same "army" as the Irish. Matt Murdock, as his secret vigilante persona Daredevil, investigates the cartels, who he learns had all of their high-power weapons stolen by a single man. At the hospital, Grotto and Page are attacked by this man and barely escape alive. Daredevil confronts the new vigilante in the rooftops near the hospital, and is shot in the head at point blank range.

Nelson finds Murdock the next morning. Though his body armor saved his life, Murdock's head and heightened senses are damaged and impaired, and Nelson insists that he rest and recover. Nelson attempts to get Grotto into witness protection, but since all of his mob contacts were murdered, District Attorney Samantha Reyes only agrees if Grotto wears a wire to a meeting with a high-level drug lord. After his senses improve, Murdock asks his armorer, Melvin Potter, for a new, improved mask, before investigating the hideout where the Irish where murdered. Realizing that they had a now missing dog, Murdock tracks it to a nearby apartment, where the other vigilante-nicknamed "The Punisher" by the DA's office-had been listening to the DA's operation with Grotto on a police radio. When the Punisher attacks the operation, Nelson and Page realize that Reyes had always meant it as a trap. Police snipers fire at the Punisher as Daredevil arrives and attacks him. Grotto escapes in the chaos, while Murdock is injured and loses consciousness.

Daredevil wakes up as the Punisher's captive, and pleads with him to stop killing, feeling that there is goodness within anyone, and that no criminal is beyond redemption. The Punisher insists that what he does is necessary, that by murdering criminals he stops them from doing wrong ever again, while Daredevil merely delays the inevitable by injuring them. Their debate culminates in Punisher bringing out Grotto, whom he caught stealing a car in an attempt to flee the city, and strapping a gun with a single bullet to Daredevil's hand, offering him the choice of killing Grotto, killing the Punisher before he kills Grotto, or doing nothing and living with the fact that his actions caused someone's death anyway. Daredevil shoots the chains holding him and breaks free, but in doing so gives the Punisher time to fatally shoot Grotto. As the dying Grotto asks why Daredevil allowed him to die, the Punisher attacks a nearby Dogs of Hell group. Daredevil manages to knock the Punisher unconscious, and then fights his way through the angry gang members to safety.

Finn Cooley, a high-profile member of the Irish mafia whose son was killed by the Punisher, arrives in New York seeking revenge, and tracks the dog Punisher took to his apartment, where he realizes who the Punisher is. Page begins investigating the Punisher herself, using files slipped to her by assistant DA Blake Tower. She learns that he is Frank Castle, once a husband and father who was hospitalized with a bullet in his head. Barely surviving, Castle escaped an apparent cover up of some kind, potentially of Reyes's doing. The Irish confront Castle at a family carousel and take him hostage. Cooley violently tortures him, until Castle escapes and brutally murders Cooley and several of the other Irish. Daredevil finds them and stops Castle from murdering anyone else, helping him escape. Castle tells Daredevil about his family, who were murdered, before allowing himself to be arrested, with Daredevil giving credit for his capture to Sergeant Brett Mahoney in hopes of restoring the public's faith in the police rather than in vigilante justice.

10 years ago, Murdock meets Natchios at a ballroom party. The two bond over their shared observational skills and thrill seeking before heading off into the night in a stolen car. They visit the boxing ring used by Murdock's late father, where Murdock discloses details about his father's death before the two spar and begin having sex midway. Sometime later, they break into the home of Roscoe Sweeney, the man responsible for ordering the death of Murdock's father. Sweeney is restrained, and Murdock beats him unconscious. Natchios urges Murdock to kill Sweeney, but Murdock is unable to, which prompts Natchios to abandon him. In the present day, Natchios requests Murdock's help on her dealings with her father's company Roxxon Energy Corporation, which Murdock refuses, though he spies on a business meeting. That night, he and Page go on their first date together. Murdock visits Natchios' penthouse, where Yakuza members begin to converge on the building. Natchios, who has stolen Murdocks' Daredevil attire, advises him to prepare to fight.

Murdock and Natchios subdue Yakuza assailants that attack Natchios' apartment. Afterwards, they talk in a diner and Murdock reluctantly agrees to continue helping her. Murdock, Nelson and Page meet with the public defender on the Punisher case, who reveals that Castle could be facing the death penalty for links to crimes outside New York. This prompts Murdock to consider defending Castle himself. Their meeting at the hospital is interrupted by Reyes, who insists on giving Castle the death penalty. Murdock confronts her, but his involvement in the case is cut short when Natchios recruits him to steal a valuable Yakuza ledger from the Roxxon building. While the two succeed in their heist and narrowly escape, Page reveals to Castle that she broke into his home and discovered private details about his family. The two converse over this until Nelson comes in and informs Castle that he has managed to shorten the latter's charges to one life sentence, as long as he pleads guilty. Castle agrees, but when stating his plea to Reyes and the judge, he suddenly pleads not guilty and threatens Reyes. When Murdock returns to the firm, Nelson informs him The People v. Frank Castle has begun.

Castle's trial begins. Murdock neglects his work on Castle's case to continue moonlighting with Natchios. The two then raid a train car and get into an extended fight with the Yakuza, only for Natchios to be severely wounded when Daredevil keeps her from killing an attacker. After, Murdock tends to her wounds and asks why she left him, only to be told he "deserves better". The next morning, Murdock is late to make his opening statement at Castle's trial and a reluctant Nelson is forced to take over for him. Murdock's relationships with Page and Nelson now continue to deteriorate. Murdock reveals his work with Natchios to Nelson. Nelson, who assumes Murdock is having an affair with Natchios, suggests Murdock leaves the case. That night, Daredevil and Natchios force a local corrupt professor to decrypt the Yakuza's ledger. It leads them to an abandoned warehouse where they discover the Yakuza are digging a giant hole.

Daredevil and Natchios are attacked by ninjas and saved by Stick. Natchios is cut by a poisoned sword and rushed back to Murdock's apartment so Stick can save her. Stick reveals that Natchios works for him, then tells Murdock about the Hand and their purpose in New York. In court, Nelson begins to sway the jury in Castle's favor. Murdock offers to take Natchios back if she will leave Stick and swear not to kill anymore. Page comes by and is devastated to see a recovering Natchios in Murdock's bed. In court the next day, Castle takes the stand and purposefully wrecks his own defense. Page and Nelson berate Murdock for allowing them to lose. Natchios tells Stick that she is leaving him to be with Murdock; Murdock and her share a close moment before he is attacked by an assassin. They subdue him and discover he is only a teenager. Natchios impulsively slits the young man's throat, much to Murdock's horror. Castle enters prison and is led by a guard to a meeting with Fisk.

Fisk arranges a meeting with Castle, who reluctantly agrees to a deal which involves killing Fisk's rival in the prison who is able to provide information on the massacre of Castle's family. Betrayed by Fisk, Castle singlehandedly slaughters a swarm of henchmen of the man he had just killed, and is placed in solitary. After an intense brawl with Fisk, Castle is smuggled out of prison, now able to find the Blacksmith, the mastermind behind his family's massacre. Frank also threatens Fisk that he will kill him the next time they meet. Murdock and Natchios fall out for good over her indifference to killing. Nelson and Murdock reluctantly agree to part ways after Nelson and Murdock collapses. Page confirms a John Doe at the carousel where the Castles died was really an undercover cop, knowledge Castle learned from his cell block victim. Daredevil learns the accountant's son is one of several children held for a medical experiment by Nobu, the now resurrected Yakuza leader. Nobu manages to escape with a device to which the children were hooked. Murdock wonders whether Stick's claim that the Hand has discovered immortality can be true.

Daredevil arranges hospital treatment for the children who had been hooked up to Nobu's blood extractor. Reyes calls on Nelson and Murdock to get information on Castle that may keep her family alive. Nelson and Murdock refuse to break attorney-client privilege, forcing Reyes to tell the whole story of the carousel massacre—a major drug deal gone awry when Blacksmith, its mastermind, failed to show, and tensions spilled into the gun fight that killed an undercover cop and Castle's family. Reyes admits to covering the entire matter up for fear of ruining her career. A firestorm of bullets riddles Reyes' office, killing her and injuring Nelson. Murdock learns Castle was taken to Fisk's cellblock and visits Fisk, where Murdock fails to blackmail Fisk into revealing his involvement. Page learns that Castle was not involved in the attack on Reyes' office, as a similar attack happens at her apartment while Castle himself saves her. Natchios kills an assassin sent by Stick to kill her. Murdock on the hospital roof prepares to confront a horde of the Hand.

Daredevil takes on the ninjas assaulting the hospital. He explains to Claire Temple about the ninjas. An attempted autopsy on one of the slain Ninjas shows the scars of a prior autopsy. The hospital board chief opts to cover it up, compelling Temple to quit after Nelson's release. Nelson ponders an offer from his occasional girlfriend to join her law firm. Page lies to a detective about the attack on her apartment but accepts police protection. Murdock confronts her and she tells him she does not think Castle was behind the D.A.'s and medical examiner's deaths. Page slips her police protection to meet Castle. He admits to using her as bait to lure those he thinks are following her. Murdock thinks Madame Gao is Blacksmith's competitor and she reluctantly sends him to the pier. He talks Castle out of killing a man claiming to be Blacksmith. Stick learns Natchios survived the hit. Blacksmith's men arrive and shoot up the boat, detonating gunpowder and exploding the ship.

Murdock stops Natchios from killing Stick as ninjas descend on them and they must fight together, but Murdock and Natchios cannot stop the Hand from taking Stick. Murdock vows to find him, while Natchios vows to kill him. Police clean up the pier mess and Page insists Castle is not dead. She tracks down Castle's commander in Afghanistan, Ray Schoonover, discovering his identity as the Blacksmith and his involvement in the drug ring that led to the slaughter of Castle's family. Castle arrives and kills Schoonover, where he discovers a room full of advanced weapons. Daredevil and Natchios track the Hand and find Stick bound and tortured. Soon, Nobu reveals himself and the Hand's true motive is disclosed, as is the missing link in Natchios' haunted past, with Nobu revealing her to be the Black Sky. A fight ensues that eventually ends with Natchios saving Stick, while Daredevil escapes the Hand with Nobu determined to stop him.

Nelson meets with Jeri Hogarth to discuss joining her firm. With Stick safe at Murdock's apartment, the Hand raids a police station for information on people Daredevil has helped. When Murdock learns of it, he fears especially for Page. Murdock and Natchios use a police transmission to find the beneficiaries the Hand rounded up. The hostages are freed, exposing a trap intended for Daredevil. Murdock and Natchios make a pact to stay together after defeating the Hand with Murdock agreeing to leave New York with Elektra. Nobu arrives and attacks Daredevil, but Natchios sacrifices herself for him. An enraged Daredevil takes on the remaining ninjas with unexpected help from Castle, who shoots the ninjas from another rooftop. Stick returns to finish off Nobu by cutting his head off, then mourns the death of Natchios with Murdock. Nelson accepts the offer from Hogarth's firm, formally ending Nelson and Murdock, and has a last drink with Page before having a final talk with Murdock. Castle burns down his family's home, after taking a CD labelled "Micro". Murdock reveals to Page that he is Daredevil, while the Hand recovers Elektra's dead body.

After being seriously injured when a building collapses on him while fighting as the vigilante "Daredevil", Matt Murdock washes out of the New York City sewer system. A taxi driver finds Matt and gets him to Father Paul Lantom who entrusts Matt to the care of Sister Maggie at the Saint Agnes Orphanage, where Matt was raised. As he slowly recovers, Matt has a crisis of faith and decides that he would rather put his life in danger and continue fighting as Daredevil than return to his civilian life. He begins training to fight again, and one night he tries to stop a kidnapping; he is beaten and almost caught by the police. Matt's friends, Karen Page and Foggy Nelson, start to lose hope that he may still be alive. In prison, criminal Wilson Fisk decides to make a deal with the FBI to protect his love Vanessa Mariana, who can be charged as an accessory to his crimes. The case is assigned to Agent Ray Nadeem, who is struggling with being unable to receive a promotion due to financial troubles after he paid for his sister-in-law's cancer treatment.

Fisk's intel leads to the arrest of the elusive Albanian syndicate's leaders, and Nadeem convinces his superiors to let him continue to work with Fisk despite his financial troubles making him a target for bribery. News of Fisk's cooperation with the FBI spreads fast, and in retaliation he is attacked in prison by a fellow inmate. Nadeem agrees to move Fisk out of prison and into home detention, but their convoy is attacked by the Albanians on the way, and most of the FBI agents are killed. Fisk is saved by Agent "Dex" Poindexter, who has incredibly accurate shooting skills. Matt tracks down the attempted kidnappers and beats them, leaving them to be arrested. Karen is assigned to report on the attempted kidnapping, which involved the well-known Neda Kazemi; after hearing about the death of Karen's brother Kevin, Neda opens up to Karen about the attack and leads Karen to believe that Matt is still alive. Foggy, who is considering leaving his well-paying lawyer job to help his brother Theo run the family business, disagrees that Matt could be alive.

Fisk is taken to a hotel that the FBI have seized, and is kept in the penthouse. News of his release from prison becomes public, prompting protests outside of the hotel and interest from reporters, including Karen who learns that the hotel had belonged to Neda's father Rostom, and that he sold it to a company that is represented by Fisk's lawyer Benjamin Donovan. Foggy goes to district attorney Blake Tower to offer his help in returning Fisk to prison, but Tower is reluctant to go against the wishes of the FBI especially because he is running for re-election. Matt investigates the hotel, and begins to hallucinate Fisk as a "devil on his shoulder". Matt interrogates Donovan and learns of the situation with Vanessa. He vows to stop Fisk and return him to prison, revealing to Foggy that he is alive but only to warn him and Karen to stay away from Fisk. During a routine psychological evaluation to determine his fitness for duty, Dex talks about the emotional support that he receives from his girlfriend Julie. However, she later appears to be someone that he is stalking.

Dex is investigated by his superiors after he claimed to kill two Albanians in self-defence during the transit attack while evidence indicates that he may have killed them in cold blood. Fisk saw him do the latter, but lies about this to the FBI and later explains to Dex that he is thankful for the agent's actions and has sympathy for the situation. Foggy, unhappy with Matt's demands, tells Karen that Matt is alive and then is convinced by his girlfriend Marci Stahl to run for district attorney against Tower to focus on Fisk and try defeat him that way. Foggy gains the support of the NYPD, who view Fisk as a "cop killer". Karen continues her investigation, and finds the name of a man involved in the company that bought the hotel: Felix Manning. Matt impersonates Foggy to enter the prison, and learns that Fisk had paid the inmate, Jasper Evans, to attack him so he could convince the FBI to move him. With the Albanians' help, Matt fights off inmates and guards working for Fisk and escapes the prison, but is driven off a dock by an unknown taxi driver.

When Fisk learns that Matt escaped from the taxi, he tells the FBI that he has a criminal fixer named Matt Murdock. Karen confronts Fisk's actual fixer, Manning, but he threatens her with his knowledge of her family, including her brother's death. Nadeem questions both Karen and Foggy about Matt, and both try to direct him towards Fisk and his crimes. Fisk reviews a file from Manning on Dex, and learns that he used his skillful aim to kill his baseball coach as a child. He was taught to be more empathetic through therapy as he grew up, but appeared to use it as a cover for his psychopathic tendencies such as the time he worked for a suicide prevention hotline and encouraged a caller to murder someone else rather than themselves. It was there that he started working with Julie and fell for her, and now he finds her working at the hotel but accidentally reveals that he has been stalking her. Fisk sees the potential for Dex to become a villain that the public can focus on rather than himself. Karen reveals to Foggy that she killed James Wesley.

Foggy assures Karen that she is still a good person after killing Wesley in self-defense. Dex confronts Fisk, who confirms that he was behind Julie's hiring at the hotel, and that he had intended to show Dex that life with Julie was not going to work; she wouldn't understand Dex, but Fisk does after killing his father while he was a boy. Matt visits Karen and asks for her help in finding Evans and using his testimony to stop Fisk. Foggy organizes with Nadeem, who has now been promoted due to his work on the Fisk case outweighing his financial troubles, to meet them at the New York Bulletin where Karen works and is planning to interview Evans about Fisk's plans. In exchange for Nadeem considering Evans' testimony, Matt agrees to hand himself over in the hopes of clearing his name. Distraught over Julie, Dex considers committing suicide, but is interrupted by Fisk who proposes an alternative; Dex instead goes to the Bulletin dressed as Daredevil, fights off Matt, and kills Evans before he can talk. Nadeem arrives in time to see Daredevil escaping.

Daredevil is attacked by the public and media, and Karen is unable to convince Nadeem that this was not the true Daredevil or that Fisk was behind the attack. When she tries to do the same with her boss Mitchell Ellison, he tells her to reveal who Daredevil is or quit. Karen later asks her father Paxton if she could go spend some time at home with him, but he says no. Foggy believes that he has worked out what Fisk is planning. Matt, angry that he put his friends in harm's way and worried about the skill of the pretend Daredevil, visits Melvin Potter, the man who created the Daredevil suit. Potter confirms that Fisk forced him to create a copy of the suit, and reveals that the pretender was an FBI agent. Potter then tries to frame Matt as the Daredevil who attacked the Bulletin, but Matt manages to escape the arriving FBI agents. After investigating Evans, Nadeem begins to believe that Fisk is manipulating them, but has no proof of this. At home, he is confronted by Matt who explains that the Daredevil attacker was a pretender and an FBI agent.

Nadeem realizes that Dex is the attacker. Dex attempts to reconcile with Julie, believing that he needs her to replace his therapist who died when he was younger. She reluctantly agrees to start talking with him, but Fisk later has her killed. Believing that Julie has abandoned him, Dex continues to mentally deteriorate. Matt and Nadeem break into Dex's apartment but cannot find proof that he was the attacker, only some recordings of his therapy sessions which reveal his psycopathic tendencies. Dex arrives home and catches them, injuring Nadeem but not being able to stop the two from escaping. Foggy thinks that he can prove Fisk is still working as a criminal, and that this will get him sent back to prison; he decides to raise these points in a debate with Tower and let Karen write about it, but instead she goes to confront Fisk. She reveals that she knows he killed his father, and that she had killed Wesley, while accidentally confirming that Matt is Daredevil. Matt later overhears Sister Maggie praying about the fact that she is his mother.

Struggling with the fact that both Maggie and Lantom had been hiding the truth from him, Matt goes to an abandoned boxing club where his father used to fight. Manning threatens Foggy's family unless he publicly apologizes for speaking out against Fisk at the debate. Karen decides to run from Fisk, and Maggie offers to help hide her. Nadeem tells his superiors about Dex and Fisk, but one, Tammy Hattley, kills the other and blackmails Nadeem into working for Fisk. She explains that Fisk had been manipulating Nadeem for the last year, and was behind the need for Nadeem to help pay for his sister-in-law's treatment. Fisk has Nadeem and Dex quietly arrest several gang leaders across New York and bring them to a restaurant where Fisk offers to protect them from FBI charges in exchange for payment. Fisk has Nadeem tell Matt about this meeting, but Matt knows that this will be a trap and instead goes to the hotel to wait for Fisk. While there, he overhears FBI agents loyal to Fisk who have discovered that Karen is hiding at the church.

Before, Karen postponed going to college because she knew that her father and brother would not be able to run their family diner after her mother died from cancer. Despite this, Karen grew bored of her small-town life and started selling drugs to students with her boyfriend Todd. One day, Kevin revealed to Karen that he had re-enrolled her in college, something that Paxton wants to celebrate with a family dinner, but this leads to an argument and Karen runs off with Todd. After getting drunk and high together, they return to the travel trailer where Todd lives to find that Kevin is burning it down. Todd attacks Kevin, and Karen injures Todd with his own gun to stop him. She quickly drives Kevin away, but crashes. Kevin dies in the crash. The local police chief covers up Karen's involvement, and Paxton asks her to leave. Now, Karen is hiding in the church when Dex arrives, dressed as Daredevil, to kill her. Choosing between saving Karen and lying in wait for Fisk, Matt races to the church and helps Karen drive Dex off, but not before he kills Lantom.

Dex has Nadeem take control of the church crime scene, and the FBI searches for Matt and Karen. They remain hidden with Maggie's help. The Justice Department drops all charges against Fisk, who announces his freedom to the public with a speech that proclaims Daredevil as the public's enemy. With Vanessa on her way back to New York City, Fisk goes to retrieve the painting she gave him when they first met; it is in the possession of Esther Falb, a Holocaust survivor whose family were the original owners of the painting. Fisk decides to let her keep it. Foggy considers reading a statement apologizing to Fisk, until he is called by Matt to help them escape the church: Foggy goes and surrenders Karen to the NYPD, which Nadeem allows, which distract the FBI long enough for Matt to escape as well. Matt, Foggy, and Karen plan their next moves against Fisk, and know they will need help. Later, Nadeem and his family are attacked by FBI agents loyal to Fisk. Matt helps Nadeem fight them off, and reveals his identity to him.

Fisk is reunited with Vanessa, who convinces Fisk to let her into the criminal side of his life. Without asking Fisk, Dex retrieves the painting from Falb and Vanessa notices some of her blood on the frame. Matt agrees to carry out Foggy's plan - working together as lawyers as they once had, they take Nadeem on as a client and organize with Tower to have Nadeem testify against Fisk in front of a grand jury. Foggy also offers to withdraw from the race for district attorney, and they get Nadeem's family to safety. Meanwhile, Karen calls a press conference to announce what Nadeem is doing so the public is aware given that his testimony would be sealed. Matt and Foggy celebrate after the hearing, with Foggy hinting that he would like to continue working with Matt like this. However, Fisk controls the jury and so the hearing has no effect. Nadeem is convinced that Fisk cannot be stopped, and returns to his home. Fisk decides it would be better not to kill Nadeem now that he is a public figure, but Vanessa convinces him otherwise. They send Dex, who kills Nadeem.

With Foggy's plan foiled, Matt returns to his and intends to kill Fisk. He kidnaps and interrogates Manning, learning that Vanessa ordered Nadeem's death, and Fisk ordered Julie's. Foggy meets with Nadeem's wife Seema, to whom he sent a video message that serves as his dying declaration, detailing all of Fisk's crimes. Matt tells Dex about Julie's death, which Dex investigates and finds her body. Fisk and Vanessa get married at the hotel, but their reception is interrupted when Karen distributes Nadeem's video on social media, followed by the arrival of Dex, who attacks Fisk and Vanessa. Matt soon joins the fight. Fisk defeats Dex, leaving him paralyzed, while Matt overpowers and beats Fisk but chooses to spare his life. Fisk agrees to return to prison and leave Karen and Foggy alone if Matt does not reveal Vanessa's involvement in Nadeem's death. With Fisk arrested, a funeral is held for Lantom. Foggy suggests to Matt and Karen that they all start working together again. Dex later goes through experimental surgery to fix his spine.

Emma DeLauro comes in contact with a secret group named Mutant X, which is a team of New Mutants and led by Adam Kane, a scientist who created the New Mutants. Meanwhile a secret agency, The GSA, led by Adam's old friend and now enemy Mason Eckhart, is created to deal with these New Mutants.

A New Mutant named Brennan Mulwray is captured by The GSA and turned into one of their agents. He however betrays them and together with Emma joins Mutant X.

While saving a New Mutant from two Russian bounty hunters who work for The GSA, Brennan is hit by a blast of an unknown weapon, which can kill him in a short time. Meanwhile, a teenager wants to sell his father and stepsister (both New Mutants) to Eckhart.

While searching for a Feral New Mutant, Shalimar meets another male Feral New Mutant and quickly falls in love with him. It turns out that he works for The GSA and used their material to create a "cure" for mutation.

A New Mutant with the ability to control computers wreaks havoc in the country. Now both Mutant X and The GSA have to search for him before he can reveal the existence of New Mutants to the world.

A deadly plague causes New Mutants to lose control of their powers. Now both Mutant X and The GSA have to work together to find a cure.

Adam leads the Mutant X team on a mission to protect Ashley Elliott, a New Mutant whose insatiable consumption of electricity is causing city-wide blackouts.

Jesse is in love with Toni Quintana, a Psionic Telekinetic New Mutant expert in computer science. Eckhart decides to contact New Mutant GS Agent Kendra MacEvoy who possesses superhuman strength, to kidnap Toni.

Joshua Valentine, a New Mutant newly disclosed that possesses uncontrollable pyrokinetic abilities, is kidnapped in his own house. Adam knows that the mother of the young boy is also a New Mutant.

Shalimar interferes three Feline Feral New Mutants trying to destroy Tricorp Botanicals. She tried to stop them, but they managed to escape. Back at Sanctuary, they were able to identify them: they are members of an international anti-terrorist organization called The Dark Star Unit fielded by Interpol who were all allegedly killed in a South American drug war fight two months ago in the jungles of Bogota.

A New Mutant able to live without sleeping is developing The Genetic Sequencer that is stolen by someone invisible. Adam traces it up to locate another New Mutant.

A former crime associate of Brennan, also New Mutant, leads Brennan and Emma to a trap arranged by agents of The GSA. This way, the New Mutant manages to develop new power. However due to a freak accident between this mutant and Brennan's powers colliding causes Emma's passive and aggressive aspects to be split into two people.

Jesse's estranged father obtains proof of the concealment of an accident related to New Mutants in a company that is actually a subsidiary of Genomex and tricks Jesse by leaving him with it. When the rest of the team learns that he plans to blackmail the head of the company or turn the information to the public, Jesse refuses to believe their story. Meanwhile, a New Mutant with hypersensitive hearing will be the manager of recovering the information for Genomex.

A New Mutant capable of infecting people by touching them with a toxin that alters their moral polarity makes appearance. She only affects other New Mutants for a minute, but with Non-New Mutants the toxin lasts permanently unless if she comes back and reverses it herself.

Emma and Brennan met an attractive New Mutant, Caleb Mathias. When he tries to absorb the vital energy of Emma, Brennan prevents it from happening. Soon, they discovered that Emma is not the first attacked by that New Mutant.

In a video in which shows the agents of The GSA capturing New Mutants in Mutant X's safehouses, Emma recognizes a friend of the university who could control computers with the mind that is working for the GSA.

Adam is accused of a crime that he hasn't committed after knowing Mark Griffin, a New Mutant with the power of enhancing and erasing peoples' memories through his memory absorbing gaze.

A former boyfriend of Shalimar, the New Mutant Zack Lockhart, joins Mutant X in a mission that leads them to trying to steal a genetic secret formula.

Shalimar and Brennan rescue a New Mutant who was being prosecuted by The GSA. In the pursuit, Shalimar turns out to be infected and submerges in a coma that shows her worst fear.

The GSA track a scorpion-based Feral New Mutant, who kills one of its members in her escape, and infects other one, Carl Ames, with New Mutant pheromones which leaves him under her irresistible sexual control. Brennan is later infected as well.

Mutant X and The GSA are filmed using their powers and fighting skills by a disgraced reporter who wants to make his comeback by revealing them to the world. This way, Mutant X and the GSA have to work together to destroy the recording before this one goes out to the light and the existence of The New Mutants is discovered.

Brennan and Shalimar interfere with a squadron of The GSA formed by New Mutants, but they have to move back when Brennan's power became uncontrollable and soon learn that all four of them are developing new powers. Meanwhile, a traitor in Genomex revives Patient Zero, Gabriel Ashlocke who is potentially the most dangerous and powerful New Mutant alive.

Ashlocke tries to revive an ancient Egyptian alchemist who possesses the power to cure him, since his mutations will kill him. Mutant X tries to prevent this, but they are unsuccessful.

Adam sends Brennan and Jesse to prevent a military official stealing a laser defense system. Nevertheless, the mission fails and Jesse has an accident that destabilizes his molecular structure. If that weren't bad enough this man intends to use Mutant X in his plot and that Jesse is the key element in completing his theft.

Mutant X chases Gabriel to a psychiatric hospital, but escapes traveling back in time to the year of 1978 where he tries to heal himself in his own ailment.

Brennan and Shalimar investigate a series of deaths for which a New Mutant is seemingly responsible. Shortly later they face a cryptozoologist who is accompanied by a group of hunters. If that weren't bad enough, the New Mutant is actually a Feral like Shalimar who is infected with a disease that makes him more Feral, and Shalimar is infected with it as well.

Gabriel Ashlocke manages to enter Sanctuary with his ally Kim thanks to his telepathic union with Shalimar. His proposal is to force Adam to heal his ailment.

A military plane is knocked down in an enemy territory, Mutant X move up to the place of the accident to recover a stolen weapon from the government that was inside the vehicle, though Brennan also wants to save the pilot due to his beliefs of not wanting the man's family to experience what he went through due to his own father being shot down and killed behind enemy lines.

When Brennan remains trapped inside an invisible city, which was founded by a man who hated the modern world, the rest of Mutant X must rescue him before he gets executed for a crime he didn't commit by the man's descendant who wants to prevent the current population from learning of the modern world. Based on The Tempest.

Mutant X realize they are being implacably chased by a group of aliens who want to capture specimens and take them with them out of the Earth.

A New Mutant able to jump from body to another uses his abilities to take revenge of Genomex and three scientists who experimented with him to prevent him to get a normal life.

When Shalimar gets injured, Mutant X decides to replace her temporarily. The problems come when her replacement decides that she wants to remain in Mutant X permanently, and they are unaware that this replacement is behind Shalimar's injury in the first place.

A former girlfriend of Brennan comes to Mutant X asking for help due to her being in danger after discovering a politician's darkest secrets. In addition, she has a surprise: she assures that Brennan is a father of her son.

Emma infiltrates a group of ecoterrorists with being discovered by the chief of the group, who is a Psionic Precognitive.

A New Mutant with the ability to shoot photon daggers from his fingertips escapes from prison and goes after Adam seeking revenge.

Jesse and Brennan go undercover to investigate a prison gladiatorial scheme. However, despite Brennan not being conformable of having Jesse with him due to his different background, he is infected with a drug that causes him to become more violent and out of control.

Adam is the target of an assassination league. After their first failure, he sends Shalimar to infiltrate the group but the situation quickly becomes dangerous for her.

Mutant X must protect a defense witness against a New Mutant who can tune into the senses of others that he had touched.

Adam is put on trial by a mysterious group called The Tribunal for crimes against humanity.

Mutant X tracks down a Pyromaniac New Mutant but matters are complicated when Emma is "possessed" by the spirit of his most recent victim, while Shalimar who felt useless earlier decides to work on fighting her natural fear of fire.

Mutant X must protect a Senator's daughter but Brennan's powers grew out of control, endangering the mission.

A New Mutant with the ability to alter a person's reality, shattering their minds in the process sets out to locate Sanctuary, and captures Shalimar to do so.

Mutant X travels to an oil rig to find The Protocanth, a prehistoric humanoid creature believed to be extinct.

Shalimar learns that her father's company is involved in genetic testing and the person backing him, has plans of his own.

In the aftermath of disaster, Mutant X find out that Emma is dead while Adam is missing, upon search they find out that Mason Eckhart has abducted Adam and Eckhart in exchange wants Adam's research to get his body in natural state. The team finds trouble unlocking Adam's files and a New Mutant Lexa Pierce steps in to help revealing that Adam's disappearance has stirred things up in the world of genetic research and that a lot of people are angry and in someways is able to convince the team that she's on their side. Eckhart reveals that Adam is dead and steals the research and later abducts Brennan to find the codes and access to Sanctuary however as he does, Mutant X comes to rescue and Mason is shot to death by an angry Brennan. The team lay over the past and Jesse discovers Lexa has plans of her own.

A prion disease weapon is put up for an auction amongst the bio-terrorists however Lexa's contact wants to keep that from happening and lets Mutant X work out the mission of getting them the weapon. The mission happens to be very challenging when they are all captured but with the weapon replaced by Shalimar they manage to escape but Lexa reveals to Jesse about a mysterious woman named Dominique who is known to be the greatest Genetic Engineer. Meanwhile as Dominique learns that weapon's missing she orders for a search against Mutant X.

When Mutant X receives an SOS message from a mysterious source they go to is a military base that has become infected with a deadly disease. The team finds out that the scientist who created the virus was an acquaintance of Adam and has ulterior motives regarding the infectious deadly virus.

Shalimar helps her friend Andrea, who is also a psionic, stop a serial killer who mimics the infamous puzzle killer and leaves clues to his next victims in the form of puzzles, though down the line when his next victim is revealed to be Shalimar, Mutant X finds out that Andrea's brain has been corrupted and she's the serial killer.

While on a night out, Lexa has been unknowingly drugged with a lethal substance that wrecks havoc on her powers. Lexa is eventually stabilized but the team soon learn that she's going to die in 72 hours unless a cure is found. As such, Shalimar and Lexa go undercover, successfully getting arrested where they end up in a woman's prison meeting Dr. Sara Stanton (Jessica Steen) who also happens to be the creator of the deadly drug Lexa was dosed with. But the mission is threatened when Stanton attempts to get her revenge against her boyfriend, Hector Friemark (David Hewlett) who is the true mastermind behind the entire drug operation and who was also responsible for Stanton getting arrested while Shalimar and Jesse must pick up the pieces and get the necessary injection required to save Lexa's life when Lexa collapses and begins suffering seizures.

An acquaintance of Brennan, Dr. Victor Palance who helped Brennan contemplate with his powers when he was young, calls Brennan to investigate bizarre deaths occurring at a local psychiatric hospital that has been reopened after a long while. Brennan discovers a New Mutant with ability to create illusions is the one who's been killing the people and posing as ghost of one the children who died in a fire long ago in that hospital.

Lexa's contact set Mutant X on a mission to locate and capture a powerful New Mutant Kristoff who possesses the power to take life and give life to someone else. However there is another group looking to capture him for themselves, and lets Mutant X into miseries that cost the life of Brennan and Shalimar but Kristoff heals Shalimar and takes the life of a framed person in his cult. Shalimar feels bad for Kristoff as he dies saving Brennan but soon takes life of a traitor to live again and Brennan learns what he means to Shalimar.

Jesse tries reconnect with his former fiancee Alisha when the team learns that her company is involved in the genetic manipulation of crops however it later turns out that Alisha's trusted executive was going behind her back to create genetically modified locusts to destroy other farm's crops to earn more money. Brennan and Shalimar with the help of a doctor from The Dominion find cure for the situation and Jesse reveals his secret to Alisha but even though she accepts him Jesse explains his new life to her and says they can't be together so she tells him to not let go of true love again.

A Tele-Cybernetic New Mutant plots to take revenge on Mutant X for putting his body in paralysis and uses his powers to takes over Sanctuary's security system and locks Brennan and Jesse inside where as Shalimar and Lexa escape. When the Mutant leads Shalimar and Lexa into a trap she realizes who they are dealing with, Shalimar finds clues to locate the Mutant and stops him before he could kill Jesse and Brennan.

When Shalimar discovers Lexa sneaking into her own missions, the team learns about Lexa's estranged twin brother, Leo Pierce who has a multiple personality disorder but as he is a New Mutant he is able to shape shift into different personalities, as he becomes the main target of an underground operation harvesting New Mutant organs, Brennan helps Lexa in finding him meanwhile Jesse and Shalimar look into Leo's history. As Lexa finds him one of his aggressive personalities Troy defeats Brennan and to save him she shoots Troy with a laser killing Leo as well.

Lexa gets information from The Dominion about a bomb that would take out an entire building. Brennan and a time-traveling New Mutant Samantha go through several alternate realities to defuse the bomb with help of Mutant X but fail every time except in the last run, when Samantha sacrifices herself to let the mission succeed.

Brennan and Shalimar investigate a mystery of a secret group working while they find a person who thinks that Mutants are aliens and everything including GSA, Genomex and Adam Kane is a conspiracy meanwhile Lexa struggles to make a decision of continuing as a part of Mutant X or leaving it since her deal with Dominion of finding her brother is over.

Lexa's contact sets Mutant X to acquire a number of paintings that has immense importance and Shalimar is given vital information from a mysterious source. Lexa finds competition in a New Mutant who has the ability to manipulate energy while stealing the paintings and teams with up him to get it and Jesse gets jealous, meanwhile Brennan and Shalimar investigate the mysterious voice and find out that the paintings contains clues to a formula of a new fuel source that can change economic powers in the world.

A man named Anthony Gervais has taken a few members of The Dominion Council hostage by putting them in state of suspended animation and is demanding a ransom to release them. Adam reveals to Shalimar that he is the mysterious voice and asks her to secretly save a scientist who discovered the process of inflicting suspended animation. Shalimar goes rogue to save the scientist meanwhile Lexa and her contact learn that Shalimar has been receiving a communication from outside. The team eventually trusts Shalimar and with Adams help the scientist discovers a cure for suspended animation and frees the hostages.

Brennan is forced to return to his criminal past when Mutant X discovers that his old partner is involved in stealing secrets from The Dominion.

Mutant X unearths an old military experiment involving an age-reversal serum and is surprised to discover that Jesse's grandfather is one of the test subjects.

Discovering that their teammate Lexa is the subject of a covert experiment that is controlling her, Mutant X hunts for the doctor who is responsible.

When Jesse's life hangs in the balance, Brennan must connect to him and lead him through past memories they've shared in order to save his life.

Mutant X must stop a rogue scientist from cloning women for use as slaves in his ultra-exclusive men's club.

Brennan battles with The Guardian of the Prophecy to stop the late New Mutant Ashlocke's plan from beyond the grave of world domination.

Lexa's suspicions lead Mutant X to unveil a traveling death camp, which is posed as a circus for New Mutant refugees and Mutant X's enemy within The Dominion.

When The Dominion captures Lexa, Jesse and the rest of Mutant X rush to help her. Later, they learn who The Creator really is.