Sydney gets shocking info on her dad's role in Danny's murder and takes on a countermission against the SD-6 to bring down an arms dealer linked to a missing nuclear weapon. Meanwhile, Will begins to grow suspicious of his friend's secret life; and Vaughn is taken off Syd's case after his mishap puts the entire world in danger.

A mission to steal an ancient sketch pits Syd against her sworn nemesis, a Russian agent who's after the same target. But when the container holding the painting proves impenetrable, the two foes are forced to team up to satisfy their respective agencies. Meanwhile, Will begins to notice something very fishy about Danny's murder; and Francie frets over her guy's possible infidelity.

Sydney and Dixon go on a dangerous case involving the safety of the United Commerce Organization. Francie confronts Charlie about his secret date with another woman, and Will continues to get closer to the truth about Danny's murder.

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 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.

Sydney goes undercover in a mental institution to get information from Shepard, a man who has been unconsciously programmed to be a deadly assassin. Meanwhile, after Sydney becomes convinced that her father was responsible for the death of her mother 20 years earlier. Will discovers the true identity of the woman who claimed having an affair with Danny and Francie is relieved to learn that Charlie is not having an affair other woman. Marshall finds the computer worm planted in the SD-6 mainframe by the CIA.

While helping Shepard escape from the asylum in Bucharest, Sydney discovers the shocking connection he has with her past. Meanwhile, after tracking the computer virus secretly planted by the CIA, Sloane is confronted by Alliance representative Alain Christophe, who suggests that one or more moles may have infiltrated SD-6. Will continues to investigate the woman claiming to be Danny's mistress and Sydney finds out the truth about her father's involvement in her mother's death 20 years earlier.

Sydney must undergo an extensive lie detector test to satisfy Sloane's frantic search for the SD-6 mole. Meanwhile, with nemesis Anna Espinosa following her every move, Sydney seeks out the connection that a device may have to the 500-year-old prophetic Rambaldi sketch. The mystery of Kate Jones deepens as Will continues to investigate Danny's death; and Sydney discovers that a keepsake from her mother Laura contains more disturbing connections into Jack's past alliances.

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 on a mission, and Will realizes that his discovery of Kate Jones' pin could uncover some unexpected information.

Sydney briefs her CIA handler, Agent Vaughn, on her recent captivity at SD-6 and is surprised when he unexpectedly gives her a Christmas gift. Meanwhile Jack has to find a way to save Sydney when he discovers that Sloane has ordered her tortured and killed for being the suspected SD-6 mole. Will may be making the mistake of his life when he begins to research a name heard on a mysterious audiocassette — SD-6.