After waking up in Tokyo, Sydney tries to remember what has happened in the past two years, and comes to shock when she discovers that Vaughn in married, and about what has happened between Jack and Sloane.
While searching for her memory, she is lead to Sark, who is in jail, but her interview time for him is shortened when he becomes bait for two CIA scientists. Also, Vaughn decides to re join the CIA, and Jack talks to a friend about Sloane's company.
Sydney and Vaughn are brought back together to prevent Sark from destroying the nation's satellite communication systems. Also, Sydney has to accompany Vaughn and Lauren to see Sloane.
Sydney finds clues about the 2 years that she can not remember from Simon Walker, the leader of a group that collect deadly weapons. During Sydney's mission, Vaughn becomes worried about Sydney, and feels confusion about his feelings towards Lauren. Also, Jack tells Dixon Sydney's secret to help her.
Lauren and Sydney fight when she finds out about Sydney's part in Vaughn's stabbing. Also, Sydney wonders about Sloane's faith when he is taken by Kazari Bomani who works in The Covenant.
Sydney's emotions become twisted when she sees Alison Dorn, who was thought dead, and is a major part of The Covenant. Meanwhile, Lauren is looking for Lazarey's murderer and leads her to find out Sydney's connection. Also, Syndney becomes Sloane's handler.
Jack tries anything to make sure that the NSC does not find out about Sydney's hug of a Russian Diplomat. But his actions hurt Vaughn's marriage to Lauren as gets closer to finding out about Sydney. Also, Sydney agrees to go on a mission with Sloane and discovers an unexpectd ally from her pars two years.
Sydney is taken by the NSC and Vaughn, Jack, and Sloane have to go rescue her. But they must rescue her before she undergoes an unsafe surgury to recap her memory. Also, Lauren is forced to chose between the NSC and Vaughn.
During a trip in the desert, Sydney makes a shocking discovery, and agrees to participate in an experimental procedure, conducted by a wild doctor, created to retrieve her memories of the past 2 years.
Sydney pulls Will out of the witness protection program in order to find the identity of 'St. Aidan', but during their mission, they run into an old enemy. Meanwhile, Sark meets his father.
Sydney finally learns about her two years missing.
Vaughn and Sydney head out to North Korea to get information from a contact, but when they get stranded there, Jack calls a woman who knows Irina to help rescue them.
Sydney and Weiss are forced to convince Tori Cummings, a security systems designer, to help them break into a Lethal Response System, so that they can retrieve the Doleac Agenda and get ahead of the Covenant.
Sydney and Vaughn are ambushed while trying to obtain a bomb. Meanwhile, Sloane tells Dr. Barnett his biggest secret, and Sark and Lauren become closer.
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.
Dixon and Sydney have to help save Dixon's children after Sark kidnaps them. Meanwhile, Lauren is forced to work with her father. Also, Sloane is framed as the CIA mole.
Vaughn and Sydney go on a hunt for Kazari Bomani to retrieve a piece of Rambaldi's map. Meanwhile, Jack tells Senator Reed his views on his daughter. Also, Vaughn decides he wants a seperation from Lauren.
Sydney and Jack tell Vaughn that they believe Lauren is the mole, but he is reluctant to believe him. Meanwhile, Sark and Bomani take the Rembalbi machine. Also, Sydney and Vaughn are forced to stop a virus from the Covenant that is hurting the world's medical facilities. And Sloane reveals to Jack his biggest secret.
Vaughn is forced to pretend he is in a 'happy marriage' when he finds out about his wife's lies and secrets. But he becomes shocked when he finds out that Olivia, Lauren's mother, is a part of the Covenant also. Also, Jack refuses to tell the CIA what may save Sloane's life. Also, Jack reveals the Passenger to Sydney.
After finding out the location of the Passenger, Jack, and Sydney request for the aid of Sloane in their search. Also, Vaughn is kidnapped and tortured by Sark and Lauren to find out the where abouts of the Passenger.
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.
Vaughn is on a mission to find his wife, and will do anything to do it. When he finds out the location of his wife, he will do anything to hug her, even though Sydney disapproves, but when the mission ends up putting Vaughn in the hospital, Sydney decides it's time to hug Lauren. Also, Nadia is forced to decide whether she can trust her father.