Sydney tries to recall her missing two years while she is updated on the lives of her friends and family.
A couple of CIA scientists are kidnapped and their capturers demand Sark as the ransom. Meanwhile, Sydney continues to try to find out what happened during her two missing years, and Vaughn decides to return to the CIA.
Sydney and Vaughn are reunited as a team. Meanwhile, Jack tries to find a way to stop Marshall from finding out the identity of a murderer.
Sydney meets a man who she thinks holds the key to her missing two years; Vaughn fights off jealousy while Sydney is on her mission.
Lauren confronts Sydney about Vaughn's stabbing, as his life hangs by a thread; Kazari Bomani kidnaps Sloane; Jack questions Simon about Sydney's missing year.
Sydney discovers that a woman who was once presumed dead is indeed alive and is a prominent member of The Covenant.
Jack ensures that the NSC doesn't discover that Sydney murdered a Russian diplomat. Sydney decides to accompany Sloane on a mission.
In order to rescue Sydney from the NSC, Jack and Vaughn are forced to work with Sloane; Lauren must choose between the NSC and her husband.
An eccentric doctor tries to retrieve Sydney's lost memory through an experimental procedure.
Sydney takes Will out of the witness protection program only to come face-to-face with Allison; Jack and Vaughn gets arrested by Lindsey; Sark encouters Dr. Brezzel.
Sydney finally learns the truth about her missing two years, but from an unlikely source.
Sydney and Vaughn's mission to help a North Korean Covenant offical defect ends with their capture after the Covenant poisons the pilots of their ride into North Korea. Irina's sister Katya offers her help in secreting the pair out of the Korean death sentence, but with a catch: she demands that Jack kill Sloane.
Sydney and Vaughn try to figue out who is killing members of the Covenant; Sloane is advised to see a psychiatrist; a security expert is asked to break into a lethal response system.
Sydney and Vaughn come under fire in the field when they try to stop terrorists with a new kind of bomb. Unknown to them, Lauren and Sark work against them at every turn. Sloane reveals that he believes he may be Sydney's father.
Sydney and Vaughn try to locate a bomb by convincing its maker that they are part of the Covenant.
Dixon asks for Sydney's help when his children are kidnapped; in order to prove her worth, Lauren frames Sloane as the mole in the CIA.
In tracking a bioweapon, Syd enlists Sloane's help to gain a location on a Omnifam truck linked with the Covenant and a key. Vaughn tells Lauren his intentions to separate. Sark orders Lauren to kill her father. Jack goes to Senator Reed with proof of Lauren's trickery.
Sydney and Vaughn act to prevent a virus from crippling medical facilities around the world. Lauren refuses to believe that Lauren could be a CIA mole.
Vaughn finds out the shocking truth about his mother-in-law, and a monk discloses the identity of The Passenger to Sydney.
Sydney and Jack ask Sloan for information that will enable their search for Sydney's half-sister; Vaughn is kidnapped and tortured.
Sydney and Vaughn continue their search for Sloane and his daughter Nadia; Vaughn is obsessed with finding Lauren.
Lauren steal classified documents from the CIA; Vaughn tracks down Lauren; a stunning revelation makes Sydney question everything and everybody.