Sydney Bristow is a young university student living an uneventful life in Los Angeles. She is recruited to work for SD-6, allegedly a secret branch of CIA. After some time she falls in love with Daniel Hecht (Edward Atterton), a promising pediatric cardiologist, and makes the fatal mistake of telling him about her secret identity. When the SD-6 finds out, they murder him to protect the secrecy of her identity. Sydney, devastated by this loss, takes several months off from work to recuperate and focus on school. Her partner, Marcus Dixon is sent to check up on her, and urge her back to work. She tells him that she is not ready yet, even though it is long past when she was supposed to return to work. In a sudden series of events, an attempt is made on Sydney's life, only to be stopped (with ruthless efficiency) by Jack Bristow, Sydney's estranged father. He reveals that SD-6 is not a CIA division, but in fact a branch of a bigger illegal organization known as the Alliance of Twelve, which seeks to make profits from stolen intelligence and weapons. The "CIA black-ops" is the cover given to most of their employees, only a select few (Jack included) know of the organization's true agenda; the rest are merely pawns whose patriotism is exploited. Sydney is sickened to learn that her father has lied to her for years, and that he is a traitor who was complicit in letting his daughter become a pawn to his colleagues. Realizing that Sloane no longer trusts her, Sydney travels to Taipei and retrieves one of Rambaldi's artifacts in order to win his trust. After confronting Sloane, giving him the artifact, and promising to return to work the following week, she regains Sloane's trust. She visits the real CIA where she meets Michael Vaughn and Eric Weiss. She prepares a written statement telling them everything she knows about SD-6. She requests to become a double agent for the CIA and put an end to Sloane and SD-6. Later, the episode's final scene shows Sydney visiting Danny's grave. There, Jack reveals to Sydney that he is not a traitor, he is working for the CIA, infiltrating SD-6 as a double agent, and that the CIA is expecting her to do the same.

Sydney returns to SD-6 as a double agent and is assigned with Marcus Dixon to travel to Moscow to retrieve some stolen files. In the process, however, she inadvertently gives SD-6 access to a nuclear weapon, which makes her travel to Cairo and face a deadly foe in order to fix things. Meanwhile, Will Tippin (a journalist and a close friend) driven by pity and a secret devotion for her, begins to question the circumstances surrounding Danny's death. He discovers weird details about the night of the murder, one being that someone had tried to help him escape by booking him a flight to Singapore. Sydney, who still can't come to terms with her father's insincerity, reconciles with him to a certain extent when she discovers he was the one who bought plane tickets for Daniel and herself.

Sydney's life is in danger as she is sent to Madrid to retrieve a 500-year-old sketch that contains a set of binary digits on its reverse, having to do with the Rambaldi artifact Sydney brought back from Taipei. SD-6 needs the sketch to decipher the key to its workings. Meanwhile, Will Tippin continues his research into the cause of Danny's death and discovers a very strange anomaly concerning surveillance cameras in the zone of Danny's apartment the night he was murdered. Will is not aware of the danger he is placing himself in by doing this, but Sydney tries to make him stop. In Madrid, Sydney meets up with her deadly nemesis, K-Directorate agent Anna Espinosa, and a fight ensues to retrieve the sketch. It ends up at a draw, as Anna keeps the key to a small suitcase Sydney has obtained. In the end they have to make an arrangement to open the suitcase together, which has the two of them looking inside the suitcase in astonishment at something that remains unrevealed.

Sydney and Dixon go on a dangerous case in Morocco involving the safety of the United Commerce Organization and an agent friend of hers dies of a gunshot. In the meantime, Francie (a close friend of Sydney's who shares her apartment) confronts Charlie, her boyfriend, about a secret date with another woman. The little circle of Sydney's friends consisting of Francie, Charlie and Will, begins to suffer from her little white lies about her job in a bank and the many sudden trips she has to make. Will continues his investigation to find the truth about the murder of Daniel Hecht and unravels more of the mystery. Coming back from Morocco, Sydney tries to know her father better by inviting him to dinner. However, he doesn't dare turn up, which makes her miserable.

Sydney's secret double agent status is jeopardized after she smuggles a biotech engineer into SD-6 from her mission in Berlin. Will meets a woman named Kate Jones who confesses that she was having an affair with Danny shortly before his death.
Vaughn informs Sydney that her father may be working for a third secret operative agency (FBI), as he begins to feel increasingly attracted to her. The CIA plants a computer worm into the mainframe of SD-6 in order to track all their progresses and obtain inside intelligence. Kevin Mitnick is a guest star of this episode.

Sydney becomes convinced that her father was responsible for the death of her mother, Laura Bristow, 20 years earlier, as she discovers both were involved in a car accident while her father was trying to escape from FBI. She also suspects he might have been a double agent for KGB. Amidst all this confusion, Sydney is made to go undercover in a mental institution in Bucharest to get information from Shepard, a man who has been unconsciously programmed to be a deadly assassin. In the meantime Will Tippin discovers the true identity of Kate Jones (Eloise Kurtz), the woman who claimed having had an affair with Danny. Francie is relieved to learn that Charlie is not having an affair with another woman but trying to be a singer songwriter and that the woman is the piano player he is rehearsing with. Marshall Flinkman, the chief technician at SD-6, finds the computer worm planted in the SD-6 mainframe by the CIA and tells Sloane, who congratulates him and tells him it was part of a special security test he's passed. Sloane now has suspicions that someone in SD-6 is a mole and this sets him on his path of finding who it is.
Sydney's cover at the asylum is blown when it is revealed that an agent from the K-Directorate is in charge there who also wants to know things from Shepard.

After helping Shepard escape from the asylum in Bucharest Sydney discovers the shocking connection he has with her past. He was brainwashed by SD-6 and programmed to kill her fiancé, among others. Sloane is confronted by Alliance representative Alain Christophe after the computer worm affair blows up, whom suggests that one or more moles may have infiltrated SD-6. Will Tippin continues to investigate the Eloise Kurtz (alias Kate Jones), who now claims to have been Danny's mistress. He makes an appointment with her, but when he goes to her place it has been emptied and repainted and she is gone. Later, she's found dead in Echo Park. Sydney, in the meantime, understands that Shepard is not really responsible for Danny's murder but he's been used by the SD-6 very much like herself. She lets him go and tells SD-6 that he went totally insane and committed suicide jumping from a bridge near the frontier with Bucharest.
Upon her return to Los Angeles, she learns the truth about her father's involvement in her mother's death 20 years earlier. It was his fault because he was fleeing from another car when they had the accident. But Syd also learns for sure that he was not involved with KGB. He tells her that during the Cold War everybody was suspicious of illegal activities, so he was investigated as a routine process.

Sydney must undergo an extensive lie detector test to satisfy Sloane's frantic search for the SD-6 mole. With nemesis Anna Espinosa following her every move, Sydney is told to find out the truth about the connection that a clock made by one Giovanni Donato for Rambaldi in the 16th century may have to the 500-year-old prophetic Rambaldi sketch with the binary digits on the back. The mystery of Kate Jones deepens as Will continues to investigate Danny's death when he finds a piece of jewelry in her abandoned car, that works as a microphone to contact someone else. Sydney accidentally discovers that some books her father gave her mother as a present have 5-character rows of Cyrillic letters imprinted at the margins, which seems to prove that he indeed had some kind of connection with KGB.

Sydney's life is placed in mortal danger when Sloane is informed by his superior that she is the SD-6 mole. Meanwhile, Dixon's life hangs in the balance after he is shot by Anna Espinosa on a mission, trying to recover a Rambaldi manuscript hidden in the mountains of South-America. Will realizes that his discovery of Kate Jones' pin could uncover some unexpected information.

Sydney briefs her CIA handler, Vaughn, on her recent captivity at SD-6 and is surprised when he unexpectedly gives her a Christmas gift. Their relationship remains halted because they both know that they can't endanger her position by going out in the open about it, but Sydney also seems to like him more than she would admit. Meanwhile Jack has to find a way to save Sydney when he discovers that Sloane has been convinced she's the mole and orders to torture and kill her. Will may be making the mistake of his life when he begins to research a name heard on a mysterious audio cassette --SD-6.

Sydney is grateful and proud of her father after he saves her life while on a case in Havana but her admiration is short lived when Vaughn discovers further evidence that Jack may have been responsible for the deaths of over a dozen CIA officers 25 years earlier, one of them his own father. After thinking it over carefully, Sydney decides to speak against her father in front of senior CIA agents. But she is surprised to see him at the meeting, where he himself tells her that yes, he was involved but he was not the assassin.
She's shocked to learn that Laura Bristow, her mother, was in fact one Irina Derevko, undercover agent for KGB infiltrated in the US to obtain intelligence and murder key agents.

When armed intruders take over SD-6 led by McKenas Cole, a man bent on exacting revenge on ex-boss Sloane, Sydney and Jack must work together to save their "colleagues". Meanwhile, Will Tippin fears that his investigation of SD-6 and its link to the murder of Eloise Kurtz (alias Kate Jones) is placing his life in serious jeopardy.

Vaughn disobeys orders and attempts to help Sydney and Jack avert the destruction of SD-6 headquarters and all its occupants. Meanwhile, McKenas Cole continues his vendetta against Sloane searching for a mysterious device. The daughter of David McNeil, a convict condemned to life for an affair having to do with SD-6, convinces Will to continue his investigation and help her imprisoned father. Vaughn helps Sydney out of SD-6 and they recover what Cole was there to get, a mysterious vial of liquid with the inscription , a recurring symbol found in Rambaldi's inventions and manuscripts.

Sydney and Dixon are sent to Las Vegas to gather information from a K-Directorate agent who has ties to the group that attacked and nearly destroyed SD-6. Meanwhile, Sydney accidentally discovers some shocking news about Francie's fiancé, Charlie, who recently had had a real affair with another woman. Will begins his journey to discover what SD-6 really is, and Jack continues to try to be more of a father to Sydney when he helps her decide whether or not to continue with graduate school.

Vaughn asks Sydney to use her friendship with Sloane's wife, Emily, to gain access to the Rambaldi manuscript Anna Espinosa took from her, and which happens to be under lock and key in a safe at Sloane's home. Will is kidnapped and told to drop his investigation of SD-6 or risk the lives of his family and friends, including Sydney's.

Sydney is tested by the Department of Special Research to discover her mysterious link to a chilling 500-year-old picture and prophecy foretold in the Rambaldi manuscript. A drawing of a woman who bears an eerie resemblance to her appears in a blank page of the manuscript thanks to the revealing substance in the vial that McKenas Cole had tried to steal from SD-6. Meanwhile, after uncovering the identity of the rogue group leader, "The Man," Sloane learns through fellow Alliance of Twelve member Edward Poole that a close friend may be working with the enemy.

While the FBI detains and questions Sydney about her past and possible ties to the mysterious Rambaldi doomsday prophecy, Vaughn and Jack must race to free her and find a way to clear her name before her cover is blown and SD-6 is made aware of the situation. Once the rescue op has been launched, in her quest to prove her innocence, Sydney shocks even her usually unflappable father when she makes a chilling discovery that may unravel the mystery of the 500-year-old prophecy –- she finds proof that Rambaldi's writings may hold more truth about an alleged weapon of mass destruction—and the fate of her own family.

While on a case to track the activities of Khasinau, also known as "The Man," Sydney runs into her ex-lover, Noah Hicks, who broke her heart and left without saying goodbye five years earlier. Meanwhile, Sydney tells Sloane that she wants to find her mother; Jack is ordered to see CIA psychiatrist Dr. Barnett to help him deal with his churning emotions after discovering that his wife may still be alive; and Will and Francie become suspicious of Sydney's activities after finding one of her airline ticket stubs.

Sloane begins to question where Noah's true allegiances lie, as passion ignites between Sydney and Noah. Meanwhile, Sydney continues to uncover new information about her mother, which disturbs Jack. A rogue assassin known as the Snowman is dispatched by K-Directorate to kill Calder. Will and Francie confront Sydney about the mysterious airline ticket stub found in her jacket.

In order to catch Khasinau and get closer to finding her mother, Sydney and Vaughn set up an undercover transaction for a Rambaldi artifact with Khasinau's representative, Mr. Sark. But Sydney's cover may be compromised when her partner, SD-6 agent Marcus Dixon is sent in to thwart the sale. Meanwhile, Will is enticed to continue his investigation of SD-6 when he learns the identity of one of his kidnappers. Emily tells Sydney that she knows about SD-6, which forces Sloane to make the most difficult decision of his life.

Will's life is about to change as he is sent to find the person responsible for leaking information to him about SD-6 - he finally finds out about Sydney's alias. Meanwhile, Sloane finds himself on the cusp of finally tracking down Khasinau when SD-6 captures "The Man's" right-hand man, Sark. Dixon becomes suspicious of Sydney's activities.

In order to save Will's life, Sydney and Vaughn must destroy a familiar looking Rambaldi device, while Jack makes a risky deal with Khasinau's representative, Mr. Sark. Meanwhile, the CIA believes that one of their own is a mole for "The Man"; the Alliance comes to a decision regarding the fate of Emily Sloane; Dixon's suspicions about Sydney intensify; and Sydney finds herself face-to-face with "The Man."

Sydney finds herself face-to-face with her mother, whose intentions for her daughter are made chillingly clear. Meanwhile, Sydney continues her search for Vaughn, not knowing if he is dead or alive after being swept away by a wall of water in Taipei. Will's life is forever changed when he learns the truth about SD-6 and Sydney's life as a double agent. Marcus Dixon must decide whether or not to inform Sloane of Sydney's suspicious activities.

Sydney must decide whether her mother's goodwill gesture was sincere or an attempt to kill her. Will witnesses Francie discussing her restaurant plans with a man whose affiliations are questionable, and Sloane is made a full partner in the malevolent Alliance of Twelve.

Sydney must outwit Sark in order to find a crucial piece of intel. Meanwhile, Jack faces Irina for the first time in almost 20 years. Will finally meets Vaughn and Sloane is haunted by his wife's death. Sloane, who drinks only water is seen drinking whiskey in his office. We are told that Emily's garden is dead but Sloane finds it in full bloom.

Sydney's dealings with her mother lead Jack to take drastic measures to ensure his daughter's safety. Meanwhile Will is confronted by a mysterious woman about resurrecting his story on SD-6.

Sydney discovers a terrifying secret when she's sent on a case to track down a new generation of weapons. Meanwhile, Vaughn suspects Jack of setting up Irina to take a fall. Sloane tells Jack the truth about Emily's death.

Sydney's trust in her father begins to fade. Meanwhile, Sydney and Vaughn may have been exposed to a deadly virus while in Taipei. Sloane, haunted by Emily's death, begins to unravel. Vaughn enlists Will to help research a case.

Sydney races to find a cure for Vaughn, but in order to find the antidote, Sydney must make a deal with Sark that could endanger Sloane's life. Meanwhile, Will continues his research for Vaughn and discovers some disturbing inconsistencies involving 20-year-old standardized IQ tests. Sydney finds out that Vaughn has a girlfriend.

Sydney, Jack and Irina must put aside their differences and go undercover as a loving family in order to seize six nuclear warheads from an abandoned facility in Kashmir. Meanwhile, Sloane announces to a suspicious staff that Sark will be working with SD-6, and later he is contacted by an unknown group claiming that Emily is still alive.

Sydney and Jack continue on a mission to take control of six nuclear warheads. Irina meets up with Gerard Cuvee and we discover where Irina's loyalties lie. Meanwhile, Sloane informs the Alliance that Emily may still be alive.

Jack meets Alliance counterintelligence head Ariana Kane, who is sent in to investigate Emily's disappearance and to discover who is trying to blackmail Sloane. Meanwhile, Marshall is sent on his first mission with Sydney as his partner.Vaughn schedules Will to take a CIA psych test. Francie gets suspicious over Sydney and Will's secretive behavior.

After completing his first mission with Sydney, Marshall's life is placed in mortal danger. Meanwhile, Ariana Kane suspects Jack as being the prime suspect in the disappearance of Sloane's wife. Vaughn learns the truth about Jack's involvement in the murder of CIA agent Haladki and Sydney confides in Francie about her feelings for a fellow co-worker.

While Alliance counterintelligence head Ariana Kane tracks Sydney in order to catch her fugitive father, Jack elicits Irina's help in finding Sloane's blackmailer. Meanwhile, Sydney and Vaughn risk exposing their covers to SD-6 when they share a romantic dinner together while on a case in France.

Sydney and Jack are confronted by the new director of SD-6, one Geiger, who replaces Sloane, whose whereabouts and intentions are unknown. Sydney learns of information that could destroy SD-6 and shut down the Alliance. Francie is killed by what looks like her doppelganger.

Sydney, Vaughn and Jack must determine whether CIA agent Lennox is who he says he is after his deep cover mission is compromised in Berlin. It is discovered that an agency has built a machine capable of replicating a human being's appearance. In this case, there are two agents Lennox at large and Sydney must discover which one is the real one and which one is fake. It is hinted that the machine has been used before to replicate someone else this way (Francie).

Sydney must make a life-defining decision regarding her future with CIA, while Sloane re-emerges and continues his obsessive quest to piece together the mysterious Rambaldi artifacts - with the reluctant aid of a kidnapped scientist named Neil Caplan. Meanwhile, Dixon's marriage is put to the test after he tells his wife the truth about his occupation.

This is the episode in which it is revealed what some of Rambaldi's mysterious artifacts really are: the pieces to build a reusable neutron bomb in the 15th century. Sloane is the one who controls it. Meanwhile, Vaughn begs Dixon to aid the CIA in rescuing Sydney, Will is called upon to participate in a crucial CIA briefing session, and Sydney notices that something with Francie is not quite right.

Sydney begins to question where Vaughn's allegiances lie when she learns through CIA Agent Yaeger that he is under investigation. Meanwhile Irina and another crucial Rambaldi manuscript—this one about the secret of eternal life—are used as bait to try to catch Sloane. It turns out Vaughn had only been investigating Irina through his own means because the Agency was slow and he wanted to see if he could catch her in a lie or discover additional information. Sydney also welcomes Dixon to the CIA.

Sydney faces off with her mother, while Emily must decide whether to side with her husband or betray him.

Sydney defies her father in her attempt to rescue kidnapped scientist Neil Caplan, while Sloane, seeking revenge for the assassination of his wife orders that Dixon's wife be taken out. Meanwhile, Allison in the guise of Francie manipulates an unsuspecting Will for his agency connections.

A Rambaldi manuscript prophesizes that an apocalyptic event involving a heart will soon take place. An agent is sent after one man in Panama in order to steal his heart. Dixon's grief leads Vaughn and agency psychologist Dr. Barnett to question his intentions, as his thirst for revenge on Sloane intensifies. Meanwhile Sloane receives a life-changing revelation from a mysterious monk in Nepal, Sydney and Dixon hunt for the killer who stole the heart from his victim.

Sydney begins to question Will's identity when he's arrested for espionage, under suspicion of being a double. Meanwhile Sark and Irina plot to recover the Di Regno heart, and Sloane makes Jack a business proposal.

Sydney confronts her mother, who reveals her true motivation. Sloane, for his part, begins to execute his new grand plan, Will struggles to figure out who's behind his set-up. Sydney and Allison have a vicious confrontation, which in turn leads to a starling revelation by Vaughn to Sydney!

Sydney confronts the enigma that represents not remembering anything from the last two years of her life and what has happened to her friends and relatives in the meantime. She confronts Vaughn, who has married someone else because he believed Sydney was dead. Sydney also learns that her father, Jack Bristow, has been imprisoned and isolated and that Arvin Sloane is a new man working as CEO for a philanthropic organization called Omnifam. Meanwhile, she is granted temporary CIA clearance on a case that may help her regain her memory.

Sydney's search for her past leads to a jailed Sark, but their Q&A is cut short when he becomes the ransom for a pair of abducted CIA scientists, whose kidnappers may be tied to the murder of his father. Jack contacts an old friend of sorts for info on Sloane's new world-peace project, and Vaughn makes a decision about his future as an operative.

Sydney and Vaughn are reunited again as a team to prevent Sark from destroying the nation's satellite communications system. Meanwhile, Jack Bristow must find a way to stop Marshall from uncovering the identity of a familiar murderer. Sydney accompanies Vaughn and Lauren as they meet with Sloane to ask for a favor.

Sydney discovers a link to her missing two years in the form of Simon Walker, the dangerous and sexy leader of a group determined on retrieving deadly biological weapons. Meanwhile, Vaughn struggles with his own feelings of jealousy and longing while Sydney is on her mission, aware of the pressures his job is putting on his marriage to Lauren. Jack takes matters into his own hands to protect his daughter, purposely revealing Sydney's deadly secret to Dixon in order to preserve her position inside the CIA.

While Vaughn's life hangs in the balance, Lauren butts heads with Sydney after learning the part she played in his stabbing. Meanwhile, Sydney further questions Sloane's allegiances after he is kidnapped by Kazari Bomani, a kingpin in The Covenant; Jack's cover is jeopardized when he meets with Simon to dig up information on Sydney's missing two years; and Marshall is sent on his second mission with Sydney, posing as a high-stakes, southern gambler.

Sydney's emotions are turned inside-out when she comes face-to-face with Allison, Francie's doppelgänger, who was presumed dead but is now a key figure in The Covenant. Meanwhile, Lauren's search for Andrian Lazarey's murderer leads her closer to discovering a connection to Sydney, and Sydney begrudgingly is assigned as Sloane's CIA handler.

Sydney accompanies Sloane on a Covenant assignment to steal the operating system for a microwave laser from the Chinese Defense Minister's office. Marshall uses a camouflaged remote-control car to disable security, allowing Sydney to break into a safe. When discovered by security, Sydney overpowers two guards, scrambles the operating system and escapes. Sloane then gives Sydney an envelope written in Sydney's handwriting, containing a key and a coded message ("34-14, 09-55/9, 23-185, 17-15/3") that points to an apartment in Rome. Jack explains that the message was encoded in a scheme used by Sydney's mother, suggesting that they were in contact during Sydney's two-year disappearance.
Meanwhile, Vaughn and Lauren go to Mexico to meet Javier Perez, one of Simon Walker's former associates, who was captured by Mexican police and who claims to have information about Lazarey's murder. They are taken hostage en route, giving Jack a chance to kill Perez and make it appear as a suicide. However, Sark later finds Lauren and provides evidence that Julia Thorne is really Sydney and that she killed Lazarey. Sark claims to be interested in avenging his father's death.
Vaughn helps Sydney escape before being arrested by the National Security Council and Lauren tells Dixon that he is no longer in charge of the task force due to his hiding of evidence concerning Lazarey's murder.
The episode ends with Sydney entering the apartment in Rome. She recognizes a nearby statue as a recurring feature in her nightmares but is suddenly arrested by police.

The National Security Council assumes control of the Task Force, with Lindsey replacing Dixon. Sydney is taken to Camp Williams, an NSC detention center used for interrogation of terrorists, and is subjected to shock therapy to coerce her into decoding a message found in her Rome apartment. Her attempt to escape fails.
Jack and Vaughn organize a rescue team with help from Sloane. They obtain blueprints of Camp Williams by infiltrating a Federal Emergency Managementfacility but Sloane is shot in the escape. Jack operates on Sloane to remove the bullet.
Lindsey blackmails Vaughn's wife, Lauren, into filing a false report on Sydney's interrogation under the threat of blackmail regarding Vaughn's involvement in Sydney's earlier escape.
Sydney is persuaded to reveal the contents of the message when a fellow inmate is tortured. However, the inmate is then revealed to be working for the NSC, who know that empathetic suffering is harder for Sydney to sustain than physical torture.
Marshall attempts to obtain access codes for Camp Williams, but they have mysteriously been deleted. With Lauren's help, the extraction team infiltrate the Camp just as Dr Vasson is about to fatally operate on Sydney to obtain information about her missing two years. Lauren helps them rescue Sydney, who reveals that she gave fake coordinates to Lindsey.

Sydney and Jack visit the co-ordinates from the coded message and find a box containing the hand of a Rambaldi follower. Lauren returns to the CIA, claiming to have been captured by The Covenant who are asking for the Rambaldi Device in exchange for Sydney.
Sydney visits Dr Brezzel, a neuro-researcher who specializes in dream memory state. Sydney is put into a drug-induced dream state and awakens in an ambulance with Vaughn watching over her. Vaughn explains that Will is going to be okay and that Francie was really Alison Doren. Sydney realizes that she is in the past and that Vaughn isn't married.
Suddenly, Vaughn changes into Sloane, who tells Sydney that she is dreaming. He then pushes her back to her apartment, representing her last memory before her amnesia. She enters her own dream and witnesses herself being taken away. Suddenly, she is experiencing her seventh birthday party, and the name St Aidan is on the cake. Lazarey appears and Sydney cuts off his hand instead of the cake.
Sydney then enters a building where her unconscious body is taken inside doors marked with the number 47. She meets Lauren, who then attacks her. Sydney says "You were part of this" but then suffers a heart failure in real life. She is resuscitated by the Doctor.
Lindsey meets Sloane, who claims to have confirmation of The Covenant's involvement in Sydney's capture. Lindsey asks Sloane for an assassin who can kill Sydney during the exchange. Lindsey shows Sloane proof that he knows Sloane's endgame.
Lauren matches the DNA from the hand with Lazarey, but the hand was alive only four months ago, so Sydney did not kill Lazarey.
Sydney enters the dream state again and is in a car with Dixon. The name St Aidan appears again. Sydney meets herself in her dream and her alternate self tells her to trust Lazarey. They fight each other and Sydney shoots herself. She enters Room 47 and utters "Oh my god!".

In her dream, Sydney sees Will and the name St Aidan. She visits Will who is now working as a construction foreman. He had thought Sydney was dead but Sydney proves her identity and tells Will that Alison Doren is still alive, working for The Covenant. Will explains that St Aidan is the name of a contact he had while with the CIA.
Sydney and Will meet St Aidan, who is really Andrian Lazarey with one hand missing. Sark appears, manages to kidnap Lazarey and tortures him for information.
Will and Sydney reminisce and become intimate. Sydney finds information that she may have a safe deposit box in an Austrian hotel in Graz. She goes there with Will and they break into a safe deposit box under the name of Julia Thorne. However, Sark gets there first and steals a metal cube. Will fights and kills Allison Doren and Sydney gets the cube back from Sark. The Rambaldi Cube contains a sample of human tissue, still active, bearing the name Milo Rambaldi.
Lindsey suspects that Jack and Vaughn know Sydney's location and arrests them. He arranges for Sloane to hire an assassin to kill Sydney when she gets exchanged for a Rambaldi device, threatening to reveal Sloane's extra curricular activities to the Justice Department. However, Sloane actually has Lindsey killed and steals the Rambaldi device for himself.

During the recap, Rambaldi's prophecy is repeated: "This woman here depicted will possess unseen marks, signs that she will be the one to bring forth my works. At vulgar cost this woman will render the greatest power unto utter desolation."
The Rambaldi Cube is taken by the Department for Special Research but is hijacked by The Covenant. Sydney is kidnapped by FBI Assistant Director Kendall, who admits that he knows what happened during Sydney's missing years but had not revealed this information because Sydney had requested him not to do so.
Kendall explains that Sydney was believed to have died and they had found remains of a body matching her DNA. Nine months later, Kendall had received a call from Sydney who had just escaped from The Covenant and wanted to return. Sydney met with Kendall and told her story. After shooting Alison Doren, Sydney had awoken in a van, held captive by a man named Oleg. Together they watched Sydney's memorial service. Oleg explained that Alison Doren had been replaced with Francie's body and that Sydney's death had been faked by extracting pulp from her teeth and injecting it into her replacement corpse before burning it.
Sydney recognizes Oleg as the man she killed in Hong Kong a week after waking up.
Kendall explains that Sydney was taken to a Covenant facility, spent six months being brainwashed and murdered a man as a test of loyalty. However, Kendall explains that, as a child, Sydney had been a part of Project Christmas, a CIA program to train and prepare children for intelligence work. The program contains a failsafe to prevent subjects from being turned. This gave her the ability to withstand brainwashing.
Sydney had wanted to escape The Covenant, but Kendall had persuaded her to return, lest her friends and family be at risk. Sydney resumed the role of Julia Thorne, keeping Kendall informed of her activities. The Covenant had wanted Sydney to obtain information about the Rambaldi cube from Lazarey and then kill him. Instead, Sydney helped fake Lazarey's death.
Kendall explains that he has always been working for Special Research, collecting Rambaldi artifacts and that Sydney is still believed to be The Chosen One. The Covenant had wanted both Sydney and the Cube to fulfill Rambaldi's prophecy. Sydney tracked down the Cube to a cave in Namibia, where Lazarey used 12 keys he had collected over 30 years. However, Sydney had to amputate Lazarey's hand, which had become trapped. Kendall had then received a DVD where Sydney explains that she is going to have her memory of the past two years erased so that the location of Rambaldi's DNA can be kept a secret. She also asked Kendall to keep this information secret from herself if she returns.
Kendall explains that followers of Rambaldi's prophecy believe that Rambaldi's DNA can be used to fertilize the egg of a surrogate mother, who is referenced in his prophecy as The Chosen One.
Sydney then looks down at a scar on her abdomen and realizes that her eggs had been stolen and that Rambaldi's child would also be her own.
A mission is mounted to retrieve the Cube, which Marshall had secretly tracked. Dixon accompanies them, revealing that he had also known the truth about Sydney's disappearance. They enter the building, overcome opposition and Sydney, against Kendall's orders, burns the equipment and the test tubes bearing her name. They find Lazarey, but Sark escapes and transmits a message telling someone to take care of his father. Lazarey asks Sydney if she knows about The Passenger but is then killed by a sniper. The sniper is Vaughn's wife, Lauren.

Sydney and Vaughn travel to North Korea to meet with a Covenant defector. Lauren passes this information to The Covenant, who then poison the pilots. En route, the pilots die, Sydney and Vaughn evade North Korean missile attacks, crash land the plane and elude the military.
Sydney and Vaughn discuss the difficulty of working together. Sydney reveals that she had slept with Will and has decided to move on. Before Sydney and Vaughn can meet the defector, Sark appears and masquerades as a CIA operative. Sydney, Vaughn and the defector are captured by the military but Sark escapes. The defector informs on Sydney and Vaughn, who are then physically abused.
Jack contacts Sydney's mother, Irina Derevko, for assistance and is visited by Irina's sister, Katya, who offers help in exchange for Sloane being killed. Jack visits Sloane but Katya first calls Sloane and warns him to back off Irina, hinting that even Jack would turn against him. Katya then contacts Jack and aborts the assassination.
Vaughn admits his feelings for Sydney before they are taken to a firing squad. Instead of being killed, one of the guards kills the other soldiers and they all escape with the defector.

The Covenant defector, Lisenker, discloses the location of the Doleac Agenda, a microdisc which contains information about the six Covenant cells. It is in a chalet with a protection system designed by security expert Toni Cummings, whom Sydney and Weiss meet while posing as diamond smugglers. They obtain schematics of the security systems, bypass the lethal response security and escape with the Agenda.
Sloane meets with CIA psychologist Dr. Barnett and reveals that he has a secret that affects the only two people he cares about in the world, Sydney and Jack.
Sark meets with Lauren and reveals that he knows her affiliation with The Covenant. He proposes that they stage a coup, kill all six cell leaders and demand ascension within The Covenant by threatening to present the CIA with access keys kept by each of the leaders. After killing the leaders, Sark meets with McKenas Cole who then reveals that Lauren had informed him of their intentions and was happy that the leaders were dead since the CIA were soon to learn of their identities. As a reward, Cole makes Sark and Lauren the heads of the North American cell.

The CIA intercepts a communication suggesting that a terrorist organization, Shining Sword, has a plasma charge weapon. Sydney and Vaughn access a secure data facility to download information but their access is cut short by a Covenant operative who escapes after a car chase. They trace the weapon to a ship but Vaughn is shot while on board.
The story is then replayed, with additional scenes showing Lauren's involvement in the operation. She had leaked information, it was her in the secure data facility and it was she and Sark that had escaped in the car. Lauren is aroused by the operation and makes love with Sark.
Back aboard the ship, Sark and Lauren attempt to stop Sydney and Vaughn. Vaughn gets the upper hand, demanding that Lauren remove her mask but before Lauren reveals her identity, Sark threatens to kill Sydney. Sark and Lauren escape, arming the weapon which Vaughn disables with Marshall's remote assistance.
Sloane meets Dr. Barnett, revealing that he had an affair with Irina Derevko and that Sydney may be his daughter.

Sydney and Vaughn must convince bomb maker Daniel Ryan that they are part of The Covenant in order to find out where he has hidden one of his devices. But Sydney discovers that her ties to the bomber could lead him on a suicide mission.
Daniel Ryan, former bomb disposal expert, has created a bomb and detonates it in public to advertise his skills and prove that the bomb cannot be disarmed. He is willing to sell the bomb to The Covenant. Based on information from Lysanker, the CIA captures Ryan, under the guise of representing The Covenant.
They reproduce a Moscow hotel in order to convince Ryan that he is dealing with The Covenant. Ryan agrees to the deal, but demands that the information be provided only to Sark on a scheduled airline flight. When the contact does not eventuate, the CIA investigates Ryan and discovers that The Covenant had killed his brother. It was Sydney who had performed the murder, during a test of loyalty (explained in Full Disclosure, episode 11). A bomb is then discovered on board the plane carrying Vaughn and Sark which will activate if the plane descends to land.
The CIA reveal their identity to Ryan but he refuses to help. Sydney sympathizes with Ryan, explaining that The Covenant also stole a part of her life when turning her into Julia Thorne. Ryan then agrees to disarm the bomb, supplying a pager code. However, this actually activates the timer of the bomb on board the plane, together with one held in the CIA office, with only 5 minutes until detonation. Ryan explains that he knows it was Julia Thorne who killed his brother.
Jack manages to coerce Ryan into providing a deactivation code and both bombs are stopped with one second remaining.

Sydney attempts to rescue Dixon's kids after they are kidnapped by Sark, Lauren's status as a double agent is put to the test when she learns that she has to work with her father, and Sloane is framed as a CIA mole.

Sydney and Vaughn must track Kazari Bomani down to get hold of a piece of the Rambaldi puzzle. Meanwhile, Jack reveals his suspicions to Senator Reed about his daughter Lauren's allegiances, and Vaughn decides what to do about his marriage.

Sydney and Jack warn a disbelieving Vaughn about their suspicions of Lauren being the CIA mole. Meanwhile, Bomani and Sark take possession of the Rambaldi machine, Sydney and Vaughn must stop a Covenant computer virus that's crippling medical facilities around the world, Sloane's secret is revealed to Jack, and Bomani begins to lose faith in Lauren's ability to carry out her Covenant missions.

After finding out that Lauren is working for The Covenant, Vaughn is told to keep up the façade of a happy marriage in order to keep tabs on his wife's activities. But he's in for a shock when he uncovers the truth about Lauren's mother, Olivia. Meanwhile, Jack refuses to help exonerate Sloane of his crimes and put in motion a stay of execution, and a monk discloses the identity of the Rambaldi "Passenger" to Sydney.

After discovering the identity of the Rambaldi "Passenger," Sydney and Jack seek the aid of Sloane, to track the "Passenger" down, which involves infiltrating a museum, using retinal scans (obtained by Arvin Sloane) from the members of The Trust. Meanwhile, after learning a secret about his father from Thomas Brill, Vaughn is kidnapped and tortured by Lauren and Sark, who are about to track "The Passenger" down themselves.

With the aid of Katya Derevko and CIA imprisoned security systems designer Toni Cummings, Sydney and Vaughn attempt to track down Sloane and Nadia. But Lauren and Sark are also in hot pursuit of them in order to uncover the secrets of Rambaldi. Meanwhile, Vaughn's obsession with tracking down Lauren is beginning to consume him, Sydney and Vaughn turn the tables on an old foe, and Katya expresses her attraction to Jack.

Lauren stages a stunning betrayal to steal classified materials from the CIA. Meanwhile, Vaughn comes face to face with his darkest demons in pursuit of his wife; Nadia must decide whether or not she can trust her father, Sloane, in the pursuit of Rambaldi's most priceless artifact; and Sydney receives a shattering revelation that will make her question everything - and everyone - she thought she could trust.

The fourth season opens with a flashback from a scene of Sydney in hand-to-hand combat on a moving train. We learn that she is on a mission to recover an isotope with a fantastic name. Sydney and Vaughn reconcile passionately after their brush with death. The plot leads directly into a second hour titled Authorized Personnel Only: Part 2.

Following the theft and delivery of an ancient sword, Sydney learns that her father had her mother executed to prevent a hitman from assassinating her. Sydney, Jack, Vaughn, Dixon, Marshall, and Nadia are recruited into a "legitimate SD-6" black ops division of the CIA dubbed "APO" (Authorized Personnel Only). The new division is headed by alleged "former villain" Arvin Sloane.

Sydney seduces an arms dealer in order to locate a stolen National Security Agency code-breaking device. Team members rescue each other and Sydney and Jack argue about telling Nadia the truth about her mother's death. Jack manipulates Nadia into killing someone by leading her to believe that the person killed her mother.

Vaughn goes undercover as a priest with a dark past. He and Sydney set out to intercept a bioweapon called Ice Five, similar to the Ice Nine in Kurt Vonnegut's novel Cat's Cradle (it causes the water in the body to crystallize instantly at room temperature). Vaughn still feels guilty over Lauren's death; he confesses his feelings with a sympathetic enemy and he bonds with her. Nadia has questions for Jack regarding her mother, Irina Derevko.

Posing as Russian nationals, Vaughn and Sydney are brought to a "village" located in Russia that resembles a typical American town. It was once used to train KGB agents in how to blend into American society, but is now being used by a terrorist cell to train operatives in preparation for bringing down America's economy using an electromagnetic pulse weapon. Marshall discovers information in a book Irina Derevko used to contact her handlers. For some reason, some Russian group is trying to find Derevko.

Sydney comes in contact with an infectious drug and suffers deadly hallucinations. Dixon tells Arvin Sloane he suspects him of having a treacherous endgame and threatens to kill him when the time comes.

Sydney expresses her full hatred for Sloane during a mission to intercept a cache of an extremely powerful explosive called Black Thorine.

Former K Directorate agent Anna Espinosa abducts and tortures Nadia. Sydney relates a Rambaldi prophecy that says that she and her sister must fight to the death. Sloane makes it clear that Espinosa is part of the Cadmus Revolutionary Front; a Rambaldi-obsessed group and will try to make the prophecy come true. Espinosa shoots Nadia, leaving her in a coma. Mr. Sark claims to have knowledge about the Cadmus Revolutionary Front and tries to cut a deal.

Espinosa's bomb is assembled and ready for sale. Sark claims to be a man of his word and helps Sydney capture Espinosa while securing his own escape. Jack wakes Nadia prematurely to gain intel on the Cadmus Revolutionary Front. When Sloane confronts him, Jack claims to be a man of his word as well.

Sydney uses Nadia's birthday dinner as a pretext for stealing the key to Sloane's secure phone. Sydney and Dixon learn that Sloane has contacted old Alliance associates. The two conspire to give the CIA a corrupted key to an encrypted database—a master blackmail list. When Sloane arranges a meeting with his old associates, Jack presents them with the key to The Index. Jack is pistol-whipped when the key does not work. Nadia rescues him. Jack and Sloane finally gain access to the list. Vaughn receives a mysterious package from a mysterious 'fake nurse' while visiting his comatose uncle in the hospital. It contains a key that leads him to a journal written by his "late" father, which contains entries after the date of Vaughn's father's alleged death.

Jack kills an old friend who is poised to receive a biometrically targeted weapon. Sydney confronts the weapon (miniature helicopter with automatic weapons fire and Artificial Intelligence) and saves an innocent civilian. Vaughn learns that his father was possibly a traitor.

Nadia's orphan past, her recruitment and her recruiter's treacherous background are revealed. In a search for his father, Vaughn meets up with none other than the headmistress of Nadia's orphanage in Argentina. Vaughn asks her if she remembers anything out of the ordinary when his father stayed at the orphanage, which she replied she said she heard him say something about "Nightingale". She asks about Nadia, also.

The episode begins in Havana. Sydney rendezvous an informant by dancing with him. The information he gives is relayed to Dixon and leads to the recovery of a hard drive from a locker. Later, Sydney's taxi driver is shot and she is captured by the informant's boss. The informant is shot in the head and Sydney is subsequently buried alive in a coffin, in the middle of a graveyard.
The hard drive turns out to have been booby-trapped by Third Faction. When inspected it detonates and releases cyclosarin. The biological nerve agent infects Dixon as he attempted to aid the technician who was inspecting the hard drive. Due to the release of the nerve agent, APO goes into lockdown mode for thirty-six hours.
Marshall, late for work, arrives at the parking lot only to be informed that they're in lockdown mode and that Sydney is trapped in a coffin somewhere in Cuba. Sydney is able to communicate with her cell phone that she still had. Because Marshall is the only one not affected by the lockdown, he is sent to Havana to find the graveyard where Sydney is buried; using a transceiver he rigged to locate her cell phone and retasking a thermal imaging satellite, Marshall finds Sydney unconscious, but alive. Marshall and Sydney's mission is extended to Berlin where the man who gave them the phony hard drive is located. Since the man knows what Sydney looks like, Marshall is sent in to get a copy of the data using a remote scanner. Marshall accidentally shoots and kills him. Over the phone, Jack instructs Marshall on how to remove the man's eyes (using a spork) so that he can access a security station in the basement and deactivate a firewall. After doing so, Sydney and Marshall rendezvous and finally obtain a real copy of the hard drive, which they deliver to APO.
In the middle of it all, Marshall must sing his baby to sleep by phone with a song about the Lanthanide series. Though his wife is an NSA employee, he can never tell her where he has been.

While searching for Vaughn's father, Vaughn and Sydney discover that Nightingale is a molecular weapons system located in a nuclear reactor in Siberia. Sloane and Jack know about Nightingale and its connection to Elena Derevko. The duo later use Sydney to have Vaughn bring the information to APO and thus make it an official mission. Meanwhile, a mysterious stranger meets with Vaughn in the UCLA library and promises answers about his father in exchange for the Nightingale's coil. Vaughn, Sydney and Jack travel to the Nightingale facility to shut it down and retrieve the coil from the weapon, however, Sydney becomes trapped in the room with the Nightingale device. Jack, Vaughn and Marshall attempt from three different locations to free her, which ultimately leads to Jack shutting down the nuclear core manually exposing himself to harmful radiation. With Sydney's help, Vaughn disappears with the coil to learn more of his father. Marshall later discovers what Jack did, but swears to keep Jack's secret.

Vaughn makes an agreement with the mysterious man he met in the episode "Nightingale", to intercept a CIA shipment of a Rambaldi manual in exchange for information on his father, Bill Vaughn. In the process, Vaughn is forced to shoot Dixon to ensure the success of the mission.
Meanwhile, Nadia informs Sydney that she's been secretly seeing Katya Derevko. When Sydney confronts Katya, she learns that Irina did not put a contract on Sydney's life at all. Sydney tracks down a message from her mother that has been hidden inside a music box. The message is the number to a bank account under the name of Arvin Sloane.
Marshall dupes Jack into signing some papers, which Marshall uses to test Jack for mutations due to his radiation exposure. The test returns positive and Marshall confronts Jack informing him of the effects this may have to people who care about him, such as Sydney if she found out, unless he goes to a doctor.
Vaughn, after the success of the mission, learns that his father has actually been dead all this time and that everything, including the journal was forged supposedly by Sloane. Later, Jack reports to Arvin Sloane that Vaughn has returned with the Nightingale coil and that the CIA was still in possession of the Rambaldi artifact. It was also mentioned that Dixon was merely shot in his vest and would eventually recover.
During the final moments of the show, a second man referred to as "Mister Sloane", and bearing a distinct resemblance is revealed in Santiago.

A physicist specializing in Quantum Electrodynamics is abducted in Kraków. In custody, Roberts, the mysterious man makes contact with "Marvin Sloane's" second in command to arrange a meeting to deliver the coil vital to what the impostor Sloane is building, but the meeting goes awry and the coil is stolen. Sloane convinces all that an impostor is responsible for the recent activities. After promising Nadia that he is trust-worthy, Sloane is allowed into DSR to examine the Rambaldi artifacts to determine the impostor's next move. Sloane loses it during the recovery mission and bludgeons a man to death for assuming that the Rambaldi technology is related to eternal life. The impostor escapes, but his power source (an immense sphere seen in the season 1 episode "Almost 30 Years") remains. This episode make mention of a fictional chemical element, Zanthium 242.

Jack seeks a doctor who might be able to cure his radiation poisoning, but the doctor cannot help him and tells Jack that he must tell Sydney. Sophia, Nadia's caretaker when she was young, calls her and she comes to Los Angeles. She reveals that she was beaten when someone came to look for Nadia. Meanwhile, Vaughn and Dixon go on a mission in Amsterdam to find an agent who might have gone rogue. Dixon's associate is actually pursuing leads on Hydrosek, a water-based weapon developed by Indonesia that could wipe out entire ecosystems and kill millions. Sloane (via Marshall) acquires intel on Sophia just to be sure she was telling the truth, but Sydney finds out. Jack and Sloane later confess that they know that someone has been watching Sydney and Nadia since they were young and acquiring information about them. It is revealed that Elena Derevko is the one who has been accumulating the information. It is then shown that Sophia and Elena are one and the same.

Jack has been hallucinating visits with Dr. Atticus Liddell, a man that Jack helped relocate in 1981. Liddell specialized in radiation therapy and is believed to be the only man capable of improving Jack's health, only no one knows where Dr. Liddell is except for Jack. When Jack wakes up in a hospital, he thinks Sydney is his ex-wife, Laura. Sloane then asks Sydney to pose as her mother to get information from Jack that will lead to where Dr. Liddell is hiding. A fake house is set up and re-created to look like his former house in 1981. He reveals openly to "Laura" that he was relocating Liddell to Helsinki. Sydney subsequently finds him and brings him to APO to help Jack.
Elena steals the Hydrosek recovered earlier and kills her ally after the heist.

"Arvin Clone" raids a monastery for a Rambaldi orchid from which an anti-aggression drug can be made, one which his power source, the Mueller Device, can reverse. In CIA custody he displays Sloane's memories. He is the product of an SD-6 Psych-ops specialist's experiment. Sloane contaminated world water supplies when he was with OmniFam, and with the orchid, the "clone's" employer can render hundreds of millions passive, finishing what Sloane failed to do. The team decides to break the imposter by imprinting him with Sloan's most painful memory—the very thing that sparked his Rambaldi obsession. Sloane re-visits in his memory his dead wife, Emily, and the time when his baby, Jacquelyn, died. Arvin Sloane must decide whether to return to Nadia and repair the damage he has done to the world or live in a dream.

Elena Derevko raids the DSR facility holding all the CIA's Rambaldi devices. The CIA traces the conspiracy back to Nadia's laptop and the bugged necklace Sophia Vargas (who was Elena Derevko all along) gave her. In a flashback Arvin Sloane and Nadia Santos visit the one man who knows how to assemble the Rambaldi device. The man is subsequently killed by Elena. When Sloane and Sydney arrive at the man's trailer they find him murdered. Sloane then betrays the CIA by knocking Sydney out and fleeing with the knowledge of Elena's location. Since Sloane is the only living expert on Rambaldi, they join forces.
To find Elena and Sloane, Jack Bristow visits Katya Derevko and promises her immunity for information on Elena's whereabouts which she then gives to Jack. Dixon, Nadia, and Sydney then infiltrate Elena's compound, where Dixon is shot by Elena, but not before positively identifying that Irina Derevko, long thought to be executed by Jack, is still alive.

The episode begins with a flashback in which Jack executes Irina 18 months prior. It was, however, not Irina who was killed and instead a double from the Project Helix. It is learned that Irina's death was an elaborate setup by Elena Derevko in which Jack was meant to execute the double to make everyone believe she was dead. The information on the double is confirmed through an encrypted file called the Blackwell File (retrieved in an earlier episode). With the knowledge that Irina was still alive, Jack, Sydney, and Nadia stage a search and rescue in Guatemala where Irina was being held.
While all this is going on, a device known as the Mueller Device (Marshall calls it the Big Red Ball) is put into place over Sovogda, Russia, the entire population of which is rioting much like the frenzied bees from In Dreams.... The Rambaldi prophecy appears to be coming true and only Irina has the knowledge to foil Elena and Sloane's plot. The team makes a HALO jump into Sovogda in an attempt to shutdown the Mueller Device. The Russian authorities have ordered an airstrike, but since rupturing the sphere would release a vast amount of toxins, time is running out.

The team parachutes into Sovogda, where they find that most of the citizens are dead. The Mueller device is floating over the tallest building, where Elena and Sloane are currently carrying out Part One of Rambaldi's endgame. The Russian Air Force will soon launch an air strike, which is when Elena will activate the signal and transmit the Rambaldi signal worldwide with deadly ramifications as global water supplies are already primed. A strike would also release deadly radiation into the atmosphere and make Chernobyl look pale in comparison — in Jack Bristow's words, "like a kitchen fire."
Sloane "betrays" Elena and leads the team to her. She is then captured and Irina makes her tell her which wire to cut on the device to deactivate it. Elena says to cut the white wire, but Irina tells Sydney to cut the blue wire. Irina then shoots Elena, killing her.
Nadia becomes infected when Elena injects her with the infected tap water, who tries to kill Sydney to prevent her from stopping the device. Sloane shoots Nadia to save Sydney's life in fulfillment of the prophecy. The Mueller device then dissolves into water and destroys the building, but the team makes it out. Jack then lets Irina go free.
The end of the episode shows Sydney and Vaughn in a car going off on vacation to Santa Barbara, where they decide they would elope. After being prompted by Irina of not having a marriage full of lies like her marriage with Jack, Vaughn tells Sydney that he doesn't want to keep any secrets from her. As they're driving he tells her his real name isn't Michael Vaughn and that his assignment of being Sydney's handler was no accident; however, before an explanation can be given, their car is hit in the driver's side door by another vehicle.

Sydney and Vaughn survive the car crash that concluded the fourth season; however, Vaughn is taken away in a helicopter by an unknown group posing as an emergency medical team while Sydney runs away. Upon returning to Los Angeles, Sydney learns that Vaughn is under suspicion of being a double agent, and the car crash was a possible "extraction".
In Mexico City, Vaughn is interrogated by a mysterious man who refers to Vaughn as "Mr. Michaux". The man wants Vaughn to decipher a piece of paper that is encoded, and threatens to hurt Sydney if Vaughn doesn't tell him what is on the piece of paper. However, Vaughn breaks free of his captors, calls Sydney, and requests that she bring his father's watch to him. After arriving, Vaughn tells her that his real name is Andre Michaux.
Vaughn then takes Sydney with him to meet a man who is in Prophet Five, a project that Vaughn's father was also in. While in Cape Town, South Africa to retrieve the book, Sydney receives a phone call from her doctor saying she is pregnant. Later, while meeting with the man in Italy, Vaughn hands over the book, but he, along with the man, are shot multiple times. Vaughn is rushed to a hospital where Sydney and he pick a name for their baby: Isabelle. Vaughn then dies after his heart fails.
Meanwhile, Arvin Sloane is in jail, pleading with Jack to get him out so he can help Nadia Santos, who is still in a coma.
Four months later, Sydney goes to London and finds Renée Rienne, or "The Raven", a known criminal and assassin with whom Vaughn had been working to uncover the secrets of Prophet Five.

Ivan Curtis, the man who assisted in killing Vaughn is tracked and captured by Sydney, Dixon, and Weiss in Amsterdam. Curtis has stolen a tube of nuridium, which Marshall believes will be used to create a bomb that could have an effect like "Hiroshima times 50." It is apparent that to locate the bomb, they would have to release Curtis and track him to it so that they can capture the bomb for APO. This is accomplished by lacing a bottle of water with a liquid tracker that Curtis drinks just prior to antagonizing Sydney to the point of kicking Curtis out of the window into a body of a water; Curtis survives, and is later tracked to a large passenger plane, where Sydney, Dixon, and Weiss intercept and secretly board. On board, Sydney finds the "bomb", but is surprised to find out that it isn't a bomb at all, and is actually a case holding a person inside of it. Later, during a confrontation between Curtis and Sydney, Curtis opens a hatch in the plane and gets sucked out to avoid being taken in and in fear of what his employers may do. Back at APO headquarters, Marshall reveals that the nuridium was being used to freeze a human cryogenically. Before identifying the person, the test site is hit and the cryogenic freezer stolen.
During the mission, Weiss informs Sydney that he was offered a promotion in Washington, D.C. working for the DSR (Department of Special Research), but is unsure if he wants to leave given the timing. Concurrently, Jack searches for a replacement for Vaughn and finds a man by the name of Thomas Grace.

Marshall picks up the trail of a hacker that he believes was involved with a hack on the NSA that blew Vaughn's cover. Tracking the hacker to Prague, Sydney is forced to partner in the field with APO's new agent, Thomas Grace. With Marshall, the three find and capture Rachel Gibson, a supposed black ops agent of the CIA working in Prague under the supervision of Gordon Dean. Similar to Sydney's life at SD-6, Gibson was lied to and was working for the very enemy she thought she was fighting.
Allying herself with Sydney, Rachel returns to The Shed, the black ops unit, so she can open up a port and allow Marshall to hack in and download their files. Rachel, however, is detected by Kelly Peyton, Dean's confidant, who subsequently blows up the entire office leaving Rachel as the only survivor of the blast.

In Monte Carlo Sydney, Tom, and Dixon infiltrate a Casino to secure "the artifact", an electronic dossier. After doing so, Sydney is intercepted while in a car by being picked up by a crane outfitted with an electromagnet. Gordon Dean subsequently calls her on her cell phone demanding the return of "Mockingbird" otherwise Sydney will be dropped hundreds of feet to her death.
72 hours before, Rachel tells Sydney that her call sign while working at "The Shed" was Mockingbird. With Rachel's help APO cracks Gordon Dean's Cayman Islands accounts. Momentarily after Dean is notified that his assets were stolen and concludes that Rachel is alive and working for the CIA. During the mission to secure the artifact, Rachel is brought along in the trunk of the car; the same car that, in the end, Dean is threatening to destroy unless Rachel (Mockingbird) is handed over to him. Sydney and Rachel are able to escape the car and cling to the electromagnet prior to Dean figuring out Rachel was also in the car and then, destroying it.
Sloane is held on trial for breaking the agreement in his pardon by aiding Elena Derevko, although he was supposedly undercover. Ultimately Sloane is pardoned after accepting the aid of a mysterious stranger with a powerful and influential employer.

Having been exonerated once again for previous crimes against the United States, Sloane asks Jack to aid him in returning to APO. Jack had already put forth a request for his return, but for limited access. APO would use Sloane's extensive knowledge and contacts in return for any aid they can give in finding a cure for Sloane's daughter, Nadia. Sloane, however, is held up from returning by a Senator, which he later threatens at the behest of his new handler: Gordon Dean.
After recognizing Renée Rienne on a surveillance camera during the theft of the "man in the box", Sydney and Thomas are sent to investigate. Rienne resuscitates the man in the box, who appears to be her father. After Sydney and Tom meet her and the man, their location comes under fire from a group of mercenaries. Meanwhile electroencephalogram records studied by APO prove that the man is not actually Renée's father, despite a perfect resemblance to him. After Sydney, Thomas, and Renée realize that the man is not Renée's father, the mercenaries succeed in extracting him. He is then brought to meet with Gordon Dean in North Korea, where he is identified as Dr. Desantis.

Rachel's family is placed in the Witness Protection Program after growing concerns that her former boss Gordon Dean may attempt to kidnap them. Afterwards, based on information from Sloane, who in turn was tipped by Gordon Dean, APO infiltrates a party in search for an electronic dossier that will give them the location of a weapons designer who has created a weapon using software referred to as the "Lasso software" that can redirect a missile mid-flight. During this mission, Rachel is confronted by a guard, however, rather than fighting she runs and is eventually saved by agent Grace.
Using the recovered dossier, APO learns that the weapon designer is holed up on an oil rig. They later come to the conclusion that the only way to infiltrate the rig is to send a female agent that can pose as the designer's weekend "companion." Rachel is selected to go solo due to Sydney's pregnancy. Amid concerns that Rachel may not be able to pull off the job on her own, Rachel is sent anyway with Sydney as a guide using voice communications. While on the rig, Rachel steals the Lasso software, however, she is confronted by Kelly Peyton, her former colleague and friend while at "The Shed". The two fight for the software, but eventually Peyton escapes as Gibson is extracted with the software.
Concurrently with these events, Sloane is secretly in contact with Dean. The information previously given by Dean to Sloane was supposed to be used so that APO could track down the designer and steal the software so that Sloane could later steal it from APO and deliver it to Dean; however, Sloane refused to turn over the software "as payment" due to Dean's right-hand assassin, Kelly Peyton, showing up and endangering one of his team. Peyton was sent to the rig to retrieve the software after Dean was hesitant about trusting Sloane to make good on this transfer.
A comatose Nadia (played by Mia Maestro), whose life may now be in more danger due to Sloane's decision, makes a cameo appearance at the episode's conclusion.

Sloane decides to betray Dean when he learns that Nadia's condition will probably not improve. They meet at a race track to exchange a network access card. The APO interrogates Dean in custody for information on Prophet 5. Yet another mysterious stranger asks Sloane to eliminate Dean. Nadia comes out of her coma for a short time after a nameless nurse leaves her room.
Sloane kills Dean during a routine reboot of the APO's surveillance network. APO misses its chance to hack the network but learns it is linked to intelligence agencies around the world. Control of Dean's cell is given to Kelly Peyton

A rogue element in MI-6 is testing an MPB (Micro Pulse Bomb) which incinerates people but leaves equipment intact. Through old contacts Jack learns the identity of the designer. Rachel goes to a conference in São Paulo, Brazil (should be Rio de Janeiro, because the conference is at a Beach Hotel, and there's no beach in São Paulo) to bug the designer's laptop. Under the cover name "Bob Brown", Julian Sark is there to do the same thing. Both do so successfully, and after a few drinks go back to his room for sex.
In Brazil, Jack witnesses an arms transaction of a much larger MPB; one that ends in an ambush. The team realizes that Sark was the leak. Rachel and Sydney hire him. Jack and his companion are taken prisoner and moved to Tunisia. Sark arranges to buy the prisoners but gets double-crossed and is handcuffed to the bomb. Rachel manages to disarm it at last.
Includes the sentence "What's a little treason between old friends?"

Sydney is abducted in Madrid. Her interrogators use memories of Vaughn to probe her mind for the secret of The Horizon — an element of an SD-6 organizational chart she saw only once. Jack traces a contact to a nursery set up in an otherwise empty building. Sydney flees her interrogation chamber to find that she is on a freighter out at sea.
Irina, currently alone and resting in the Philippines, is revealed to be the person behind Sydney's abduction and interrogation.

After fleeing from interrogation and learning she was on a freighter at sea, Sydney goes to the communications room and sends a message to APO routed through the CIA to her whereabouts. Unbeknownst to her at the time, the message was intercepted by a mole at the CIA working for Prophet Five, although APO was able to obtain a piece of the transmission. Wanting to retrieve Sydney, APO attempts to break into a secured server room located at Langley with the goal of obtaining the remaining part of the transmission. Problems arise, however, when APO is forced to take the hard drive, which triggers an alarm. They manage to escape the situation thanks to Weiss who aids them in sneaking past the guards.
Although the transmission on the hard drive is corrupted, APO is able to learn who corrupted it. Jack sets a meeting up with the division heads of the CIA and is quickly able to identify that the mole was Davenport, who confesses to Jack Sydney's whereabouts. APO then mounts a rescue to retrieve Sydney from the freighter; however, while they are in transit, Sydney is forced to go into surgery. When APO arrives, Sydney is alone on the freighter. After analyzing Sydney, doctors conclude that Prophet Five was not trying to hurt the baby, but actually save it.

Because of the possibility of moles within APO, CIA Director Devlin shuts it down. Jack remains determined to continue investigating Prophet Five and Sydney reveals to Jack "Leo-47 Norte" as the code that Prophet Five wanted to know of when they captured her. It turns out to be an old SD-6 mission that took place in France.
Irina meets with Sydney and reveals her own knowledge of Prophet Five; the group captured Sydney thinking she knew something about "The Horizon". After Jack has Marshall hack into CIA archives for more information, Dixon and Renée Rienne force Jean Bertrand to reveal more about "The Horizon", which is stored in a safety deposit box in a Vancouver bank.
Jack, Irina, and Sydney infiltrate the bank and retrieve "The Horizon". However, Irina has leaked the information to Peyton, who arrives in the building with her men and kills the guards. Irina attacks Jack, who has "The Horizon" and Sydney realizes Irina arranged her kidnapping. When Irina insists that Peyton will kill her too, Jack responds by saying he will kill Irina first.
After Jack incapacitates Peyton, Sydney goes into labor. Jack and Irina help Sydney give birth to a girl, after which Irina escapes with "The Horizon." Meanwhile, in Bhutan, a monk receives a message from a horseman and shares the news of Sydney's infant daughter with Michael Vaughn.

One month after the baby is born, Sydney is taking time off from work. Meanwhile, Kelly Peyton arranges for Anna Espinosa, Sydney's old enemy, to be released from prison and kidnap Will Tippin, who is still in the Witness Protection Program. The kidnapping is a ruse to draw Sydney away from her sabbatical. During the rescue, Anna and Sydney fight and Anna draws a small amount of blood from Sydney during the melee and escapes. APO discovers that Prophet Five implanted a miniature bomb at the base of Will's skull, which is set to explode if Sydney does not deliver Page 47, a Rambaldi artifact, to Anna aboard a train in Portugal. Accompanied by Will, Sydney attempts to defuse the bomb and stop Anna from getting away with Page 47. During the subsequent battle, Anna locks Sydney in a baggage car where is she sprayed by an unknown chemical agent. She is rescued by Will, but in order to prevent the bomb in his head from exploding, Anna has to be allowed to escape.
Sloane is introduced to the leaders of Prophet Five who require him to undertake one last mission before they give him the cure for Nadia. As the episode concludes, Anna undergoes a version of the Project Helix protocol, emerging as a genetic duplicate of Sydney Bristow.

His obligations to Prophet 5 complete, the organization gives Sloane a hypodermic needle containing a Rambaldi-designed drug that will cure Nadia's comatose condition. But there is a price; in order for the drug to work, Nadia must be rendered clinically dead for 30 seconds. Elsewhere, the hunt for Anna Espinosa continues, with APO unaware that she is now a duplicate of Sydney. Sydney and Renee attempt to track Anna's movements during a ruse at a call centre in Jaipur; after Renée uses a clever deception to allow Sydney to complete the mission, Sydney offers her a job at APO. Renee refuses. Later, Sloane smothers Nadia to death in her hospital bed; Jack arrives and, thinking Sloane is committing euthanasia, nearly prevents him from administering Rambaldi's drug in time, but Nadia is successfully revived with no apparent ill effects from her year-long coma. When Sloane says he got the cure through contacts in Barcelona - location of the headquarters of Prophet Five - Jack gets suspicious.
Later, Nadia is reunited with Sydney, but still harboring continued anger towards her father for his past actions, particularly at the end of Season 4, chooses to live with Sydney and the baby instead of Sloane. In France, Renée seduces and later interrogates an old contact who has been given Rambaldi's Page 47 to decipher, but learns the artifact is a fake. Back in Los Angeles, Jack is about to follow Sloane to a possible Prophet Five rendezvous when Nadia appears and asks to go along. The rendezvous instead appears to involve Sloane recovering a suitcase full of Nadia's old clothes from a storage locker. Jack admits he may have misjudged Sloane.
In Ghana, where Renee's contact is to meet with Anna, the APO team waits in ambush, but the vehicle apparently containing Anna speeds off at the last second. When Sydney kills the driver it's discovered that Anna has again escaped. Nearby, Renee has been waiting with a sniper rifle to shoot a tranquilizer dart into Anna; called off the mission, she is about to leave her hiding place when she encounters Anna, who looking like Sydney, pulls a knife and slashes Renee's throat.
Back in L.A., Sloane opens the suitcase he retrieved and under a pile of clothing is the original Page 47. As he examines it, Nadia arrives, intending to make amends with her father. But when she discovers that he has Page 47, years of resentment over his obsession with Rambaldi's prophecies boil over and she attempts to destroy the document in the fireplace. The paper, however, does not burn; instead the Rambaldi symbol begins to glow on the page. In a desperate move to rescue the page from the flames, Sloane pushes Nadia away. She falls through a glass table with a shard slitting her throat and killing her. Sloane, realizing this must be part of his destiny, joins Prophet Five to await Rambaldi's endgame as Jack discovers Nadia's dead body.

An autopsy of Renee Rienne reveals that she has a chip implanted in her body. The chip is engraved with Michael Vaughn's real name, Andre Micheaux, and contains what appears to be corrupted code. Sydney makes plans to travel to Nepal to meet with Vaughn.
At the Nepal airfield, Anna-as-Sydney intercepts Sydney's contact and learns from him that Vaughn is still alive. A substitute contact intercepts Sydney and diverts her, almost killing her in a car crash.
Anna meets with Vaughn and shows him the chip. Vaughn figures out that the other half of the chip is implanted in him and he and Anna remove it. The two halves of the chip snap together and reveal the location of a hidden bunker in Germany. Anna and Vaughn travel to Germany. Sydney, having escaped from the phony contact, follows.
Anna and Vaughn locate the bunker and break in through the basement of an adjoining jewelry store. There they discover all of the intel gathered on Prophet Five by Vaughn and Rienne's fathers. Vaughn reveals that he knows Anna is not Sydney and they fight. Anna gains the upper hand but Sydney shoots her in the head, killing her. Vaughn is finally able to return home.
Sloane is working to decode the recently revealed message on Page 47. As he works, an apparition of Nadia appears, taunting him. Sloane states to Peyton that he needs a certain book to complete his work and dispatches her with a message to the bookseller. The apparition of Nadia reveals that Sloane has already completed the decoding; indeed, the note to the bookseller is actually a protocol to contact Julian Sark.

Sydney meets with Sloane, who thinks she is Anna, in order to find out what he knows about where the last Rambaldi clue is located. She tells him that she killed Sydney by shooting her in the back and that there was nothing special about how she died. On the way to Rome, Sloane talks to Peyton, telling her that he wants to kill Anna (Sydney) once she has finished helping him recover the final clue.
In a sports betting bar in Rome, Sark, who also thinks she is Anna, meets with Sydney. After calling the police himself, Sark acts out a dramatic robbery in the bar in order to get both of them arrested; this is how they will get into the prison where the final Rambaldi clue is located. It is where Rambaldi himself spent his final days. In separate cells inside the prison, Sark fakes a seizure so he will be taken out of his cell and able to unlock the prison doors for Sydney. When Sydney gets to the prison basement she meets an old man, who gives her a necklace complete with a red pendant, the final Rambaldi clue. The old man does not say who he is, but says that he is not part of the battle which is about to take place. Sydney goes back up to her cell intent on taking the clue for herself, but Sloane appears and surprising her with a stun gun takes the necklace. He then tries to kill her - as he still thinks she is Anna - by choking her, but Vaughn shows up just in time and Sloane flees.
Back in Los Angeles, Vaughn and Sydney are looking over Isabelle and talking about her when the phone rings. Sydney answers; Sloane is on the other end. He says he knew it was she who killed Anna and not the other way around. He then says he has all the artifacts and can now go through with his endgame.

With the collected Prophet Five documentation at hand, APO spreads out across the globe to take photos of the different Prophet Five members. Once they gather the photos and information at the office, they decide to make the arrests simultaneously to avoid tipping the rest of the members off, including Sloane. Jack tasks Marshall to track all their activities so they can coordinate an arrest.
Sloane talks to Sark and Peyton and proposes that they solidify their position in Prophet Five so they would be less expendable. In spite of Peyton's initial hesitation, she agrees.
Tom visits Rachel in her apartment. She consoles him in his sadness and he leans in to kiss her. When Rachel goes in the kitchen, Tom leaves. Rachel is abducted by Sark. Around the same time Marshall is abducted from his home and is brought to Sloane's hideout. With Peyton, Sloane asks Marshall to hack into the government system and locate an underground cavern by accessing the federal ground-penetrating satellite. When Marshall refuses, Peyton tortures him; elsewhere, Sark tortures Rachel.
Sydney and Jack visit Carrie, Marshall's wife, who called them for support in finding Marshall. When Sydney reveals to her that Marshall is still working for the CIA, Carrie volunteers to help and provide technical support in Marshall's absence. As soon as Carrie arrives in the APO office, she cracks the password for Marshall's program to track Prophet Five members (which is Moonglum of Elwher).
Sloane confronts Sydney in the parking lot as she is carrying Isabelle. Sloane tells her to talk to Marshall, who is determined to not give in. Sydney then tells Marshall to do what Sloane says and asks what he wants to tell Carrie. He asks Sydney to tell Carrie to finish reading the book "The Littlest Fish" to their son.
Marshall tells Rachel that he needs her help in doing Sloane's bidding. To ease Rachel's confusion, Marshall tells her that he had spoken to Sydney. Marshall suggests that they leapfrog across the network so they would not get caught in their hacks. With an understanding that Marshall actually wants to get caught, they begin to work on their laptop. Later, Rachel locates the cave that Sloane wanted in central Italy.
Vaughn relays Marshall's message to Carrie, where Carrie figures out that the lead character in "The Littlest Fish" is named Noah. She concludes that Marshall must be referring to NOAA, the National Oceanic and Atmospheric Administration - something that Marshall must be hacking currently. Carrie sets up trip wires to monitor government hacks and pinpoint Marshal's location. She finds Marshall deliberately triggering network security protocols. She narrows his location down to Ixtapa and Jack sends a rescue team.
In the basement, Rachel picks her handcuffs with an underwire and with Marshall, they escape the guard who was sent to kill them. Followed by other guards, they run through a corridor in time to be rescued by APO.
At the APO office, Carrie reports to Jack that based on Marshall's tracker, The Twelve seem to be gathering in Zurich. Jack assumes that Sloane must be presenting the information that Marshall and Rachel uncovered and assembles strike team. Retrieving information at Sloane's safehouse, Rachel mentions that Sloane is going to Umbria. Sydney realizes that he must be going to Mount Subasio.
Sydney and Vaughn travel to Mount Subasio and Sydney rappels into an icy underground cavern, where she finds Sloane with the Rambaldi amulet. When Sydney holds him at gunpoint, Sloane says that a shot will trigger a cave in. Meanwhile, in Los Angeles, Sark sets a timer for a planted bomb.
At the APO office, Tom reports that based on the files in Sloane's hideout, bombs are being planted around the APO office through the subway system. Jack tells them to clear the office while Tom and Dixon sweep the tunnels for the bomb. Marshall and Rachel are tasked to evacuate civilians. Later, Tom finds the bomb and reports that it can't be dismantled because of the fail-safe components. He suggests freezing the timer with liquid nitrogen to extend the countdown.
Peyton goes to Zurich and meets with The Twelve. Standing in the middle of the room and expected to present the amulet, Peyton opens the briefcase and pulls out two semi-automatic weapons. She kills all the members of The Twelve and their bodyguards.
With the last of the civilians cleared out of the tunnel, Jack tells Tom to get out of the train and run to safety. Instead, Tom asks to be patched to Rachel. He tells Rachel that if they had more time, he would have asked her out. Rachel tearfully replies that she would have said yes. The bomb detonates, destroying APO headquarters and killing Grace.
Sloane holds the amulet against the light. He tells Sydney she is not allowed to see it and he shoots the icy ground she is standing on. Syd falls through and is rendered unconscious.

Vaughn finds an unconscious Sydney and administers CPR. In a flashback, Sydney recalls the time when Jack told her that her mother had died, asking her to be strong. Sydney wakes up.
Peyton tells Sloane that she was able to make contact with their ally in Hong Kong, and that they have a deal as she reveals the Horizon. Sark asks if they want to go through with this global genocide. Sloane confirms as they look on nuclear missiles.
In the safety of a hotel in Siena, Sydney flashes back to her childhood when she assembled building blocks, not realizing that this was part of Project Christmas - meant to test people's aptitude for being operatives.
Later Sydney reads a report of two stolen missiles and assumes Sloane's involvement. Sydney concludes that if Sloane had killed all Prophet Five members, he must have all their assets, and would have bought these missiles from someone. Marshall then hacks into the Russian bank network and looks into the phone records. Via satellite, they are able to locate Peyton.
Vaughn, Dixon and Sydney interrogate Peyton, and she tells them that she does not know where the missiles are stored now but she knows that Sloane is targeting two cities with high civilian concentrations. Jack remarks that Sloane is not interested in devastation -he wants to profit from the reconstruction. Sydney discovers that Sloane is in Mongolia.
As Sydney prepares to fly to Mongolia, Rachel reports that she and Marshall are trying to hack into optical satellites to locate the missiles. They realize that Sloane has hacked into the network with information uploaded from a contact in Hong Kong. Peyton reveals the contact under interrogation by Dixon.
Sloane and Sark go inside the cave in Mongolia. Later, Sloane says that the next step is for him alone to do. Sloane journeys down to a chamber that turns out to be Rambaldi's burial place. He places the Horizon on top of Rambaldi's tomb. A red sphere (similar to but probably not like those generated by a Mueller device) appears and a red fluid drains from that sphere into the Horizon.
Vaughn, Sydney and Jack infiltrate the camp set up outside of Rambaldi's tomb. Sydney sneaks into the underground chamber and holds Sloane at gunpoint. Meanwhile, Vaughn and Jack are surrounded by Sark and his men. Sydney is about to destroy the Horizon when Sark arrives holding Vaughn and Jack hostage.
Holding Sydney at gunpoint, Sloane urges her to give the artifact back. He then shoots Jack. Sydney drops the Horizon and rushes to her father as Vaughn fights with his captors. Sydney shoots Sloane several times and Sloane falls into a pool of the red liquid. He dies and Sark picks up the Horizon.
Sydney flashes back to a memory of telling her father she'd started working for Credit Dauphine and Jack telling her to quit immediately.
Sydney and Vaughn carry a severely wounded Jack out of the chamber where they attempt to perform first aid. Vaughn says Sloane is dead and that Sark must be taking the Horizon to their contact in Hong Kong--Irina Derevko.
Jack urges them to go to Hong Kong. When Sydney wants to stay, Jack says that she is the only one who can stop her mother. He adds that he never wanted this life for Sydney, but Sydney is far too driven and strong to let anyone stop her. Sydney tells her father that she loves him and leaves reluctantly.
In Hong Kong, Sark delivers the Horizon to Irina and reports that the missiles are ready. Irina tells him to target London and Washington D.C. Sark goes to a control room and initiates the countdown.
Sydney arrives and confronts Irina, who tells her that power is the only currency and that through Rambaldi, they can live forever. Sydney and Irina fight furiously, while Vaughn breaks into the control room and shoots Sark. With Marshall's help, the launch is aborted.
Meanwhile, in Mongolia, Sloane's bullet wounds heal and he is restored to life. As he sees Nadia's ghost, he starts to walk out of the chamber when a wounded Jack stops him. Sloane says he can heal Jack; Jack refuses, saying Sloane has caused Sydney so much pain he won't let him do it again. Sloane tells Jack that he is now immortal, but Jack points out that he can keep him in that underground cave with him. Jack sets off explosives, causing a cave in.
Sydney and Irina continue their struggle on a roof deck, where Irina falls to her death as she tries to grab the Horizon.
In Mongolia, Sloane is half-buried alive, with no one to hear his calls for help. Nadia's ghost appears to tell him that she can do nothing for him and that as he had said, he has all the time in the world. "At least I'll have you to keep me company," he remarks. She says no as she turns her back to her father and disappears.
Flash forward to a scene of 7-yr old Isabelle playing by the ocean. Dixon arrives, and Vaughn and Sydney greet him, with Sydney carrying a toddler son named Jack. Dixon asks Sydney for some help in an assignment, but Vaughn suggests discussing this after dinner. Meanwhile, Isabelle finds wooden building blocks -- the same ones that were used in the Project Christmas tests. Isabelle assembles the blocks effortlessly and successfully, but then knocks them down nonchalantly and runs out with Sydney, Vaughn and Dixon for a walk by the beach.