When Sydney is taken into custody by the NSC honcho Mr. Lindsey, Jack and Vaughn have no choice but to ally themselves with Sloane to rescue her. But with only hours to spare before she is forced to undergo a radical surgery to recover her memories, they must put together an extraction team, headed by freelance operative Brill. Meanwhile, Lauren faces an impossible choice: side with the NSC who she wants to believe is doing the right thing, or with her husband in their rescue of Sydney.

After finally discovering the identity of the Rambaldi "Passenger," who is Sloane's illegitimate daughter, Sydney and Jack seek the aid of Sloane, to track the "Passenger" down, first by Sloane meeting with the five key members of a secret government group called "The Trust" to gain access to a Rambaldi device to locate the "Passenger". Sydney then travels to Chechnya to a prison where she finally finds her half-sister, Nadia Santos, an Argentine national and secret agent in hiding. Meanwhile, after learning a secret about his father from Thomas Brill, Vaughn is kidnapped and tortured by Lauren and Sark, who are about to track "The Passenger" down themselves while Dixon, Weiss and Marshall race against the clock to find Vaughn before he is killed.