After discovering the identity of the Rambaldi "Passenger," Sydney and Jack seek the aid of Sloane, to track the "Passenger" down. 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.

With the aid of Katya Derevko and CIA imprisoned security systems designer Toni Cummings, Sydney and Vaughn attempt to track down Sloane and Nadia. But Lauren and Sark are also in hot pursuit of them in order to uncover the secrets of Rambaldi. Meanwhile, Vaughn's obsession with tracking down Lauren is beginning to consume him, Sydney and Vaughn turn the tables on an old foe, and Katya expresses her attraction to Jack.

Lauren stages a stunning betrayal to steal classified materials from the CIA. Meanwhile, Vaughn comes face to face with his darkest demons in pursuit of his wife; Nadia must decide whether or not she can trust her father, Sloane, in the pursuit of Rambaldi's most priceless artifact; and Sydney receives a shattering revelation that will make her question everything - and everyone - she thought she could trust.

Rachel receives a little help from Syd for her first solo mission while Sloan is back at APO in frequent contact with Gordon Dean.

Sydney and APO attempt to discover whom Gordon Dean is working for and what their end game is. Meanwhile, when the group claiming to have a cure for daughter Nadia continues to play mind games with him, Sloane struggles for control.

While the gang starts to learn more about the Prophet 5, Sloane is distressed to learn that Prophet Five's cure for Nadia is just as likely to kill her. Meanwhile, Devlin returns, the search for Anna Espinosa continues, Rambaldi's prophetic Page 47 resurfaces, and Sydney offers Renée a job at APO.

Marshall reports to Jack that a microchip, found in Renée Rienne's body, is etched with the name 'Andre Micheaux'. Peyton tells Sloane that Sydney is being sent to Nepal to meet with someone regarding the chip. Sloane sends Anna, now Sydney's doppelgänger, to intercept. When Marshall discovers that the APO office is bugged, Jack frantically tries to reach Sydney to warn her before it is too late.

In the first part of [the] Alias two-hour finale event, 'Reprisal,' Sloane takes Marshall and Rachel hostage in order to discover a crucial clue to Rambaldi's ultimate endgame, as Sydney, Vaughn and APO race to stop him.

Peyton tells Sloane that she has made a deal for the Rambaldi Sphere with an ally in China. Sloane arranges for stolen missiles to be sent to Hong Kong. Sloane's plan is revealed to the APO members, who race to stop him before he can use the Rambaldi Sphere to put the plan in motion. But this all leads to a long awaited confrontation between Sydney and Irina.