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.

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 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 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.

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 fears that his investigation of SD-6 and its link to the murder of Eloise Kurtz is placing his life in jeopardy.

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