Secret Service Agent Riley Neal (Meghan Ory) is brought into the U.S. Cyber Command and tasked by Lillian Strand (Marg Helgenberger) with the assignment of protecting Gabriel Vaughn (Josh Holloway), an ex-Delta Force operative with a chip implanted in his brain that allows him to access the global information grid. The US Cyber Command investigates the kidnapping of one of its top scientists Shenendoah Cassidy (John Billingsley) in relation to a second chip being created, and Gabriel searches for his missing wife.

After a suicide bomber blows up a US Marine outpost in the Khost Province of Afghanistan with an undetectable bomb he ingested, the US Cyber Command is tasked with investigating the threat of a second attack using the same type of explosives. Meanwhile, in the process of investigating, Gabriel meets face to face with his missing wife for the first time since she went undercover.

Gabriel and Riley are tasked with finding Kate Anderson (Annie Wersching), a high level CIA analyst who fled the country with sensitive intelligence, before it falls into the wrong hands. Meanwhile, Gabriel discovers that Mei Chen is alive after her operation and has the capability to be inside his mind using her new and improved chip.

Gabriel and his team are assigned to rescue two freelance journalists (Tania Raymonde) captured by the Syrian Armed Forces before they are executed on national television. Meanwhile Riley must work with her ex-boyfriend and the truth about their past is revealed.

Gabriel and Riley search for the daughter of a senator and her friend, who have been kidnapped by Hector (Carlos Sanz), the boss of a Mexican cartel, who demands that the senator ends the sale of a U.S. spy satellite to Mexico in exchange for the safety of his daughter and her friend.

Gabriel and the CyberCom are tasked to investigate the outbreak of a deadly virus in Texas caused by a man who was thought to be executed for killing 2 police officers. In the process they discover a conspiracy involving the Defense Intelligence Agency's research into bioweapons

Worldwide, scientists working on nanotechnology and artificial intelligence are mysteriously dying of internal bleeding, which are caused by nanites. When one of their prime suspects is also killed, the suspicions turns to one of the Doc's former students. Doc himself gets infected but after some tense moments they are able to save him. Meanwhile Gabriel and Riley go for a late night snack.

When several members of Bolivian government's opposition are being assassinated, Gabriel & team are sent to protect the last one, the candidate preferred by the US government. Its learned that the assassin was Gabriel's best friend and a former Delta Force operator. But things are not what they seem and they join forces to protect the candidate and the US Under-Secretary of State.

Jin Cong escapes from Chinese prison and unleashes an EMP on CyberCom, causing Gabriel to receive amnesia through the chip, and captured the complex, intent on retrieving the Athens list, a list of children with the same genetic mutation required to operate the chip. Worse yet, he alters CyberCom files to manipulate Gabriel into working for his side.

The Witness Protection Database has been hacked and the perpetrator begins blackmailing individuals from the list into making a paralytic chemical bomb, sending Gabriel, Riley and Lillian to San Francisco to track him down.

When an advanced cyber-worm infiltrates a power grid in Los Angeles, Gabriel and Riley are tasked with tracking down the elusive hacker and preventing a nuclear meltdown.

When the former intelligence head of CENTCOM, the deputy director of the FBI and his bodyguard are assassinated, US CyberCom is asked to look into it. But when Gabriel cyber-rendered the last few minutes of the CCTV footage, he sees himself in it. The DNI places Gabriel in 'protective custody' to see if the chip was hacked and whether Gabriel was remote-controlled into doing it. But Gabriel and Riley escape and along-with rest of the team they catch Mei-Chen. But when the team meets Lillian, Gabriel is shot and someone tries to shoot Mei Chen. Mei Chen then reveals that she was hired by someone in the US Govt. to frame Gabriel.

Continues from the previous episode. A wounded Gabriel directs Riley and Mei Chen to his mother's house, a former combat nurse. While his mother treats his bullet wound, Mei Chen and Gabriel co-render. Mei Chen reveals that a governor and possible Presidential nominee could be the target of an assassination. It is later revealed that Weatherly, the Director of National Intelligence is a sleeper agent for Iran and he is one behind all this. As he attempts to kill the governor, Gabriel and Riley arrest him. Later Mei Chen is contracted to kill Weatherly in the floating prison by Leland Strand, Lillian's father.