After learning that the man she has known as Michael Vaughn is under investigation and suspected of being a double agent for another secret terrorist group called Prophet Five, Sydney begins to question whether their business and personal relationship over the years had all been a lie. When she discovers that she's pregnant with Vaughn's baby, she becomes determined to uncover the truth about him. Meanwhile, because of Jack's past betrayal by Irina, he begins to worry that his daughter may suffer the same fate that he did.

Four months after Vaughn's murder by the traitorous Gordon Dean and his associate Ivan Curtis, a grief-stricken Sydney teams up with Renée Rienne, a French freelance assassin and fugitive on the CIA's most wanted list who knew Vaughn from their past association with Prophet Five, to ask for leads in order to track down the killers before they can strike again. Meanwhile, Jack enlists a reluctant new agent, Thomas Grace, as Vaughn's replacement at APO, and Weiss struggles to decide whether or not to accept a promotion that would force him to move to Washington D.C. and leave his colleagues at APO. During this time, Sydney, Dixon and Weiss travel to Amsterdam to track down Curtis who is in the process of buying a potential weapon.