Sydney quits the CIA and joins a Black Ops unit called "Authorized Personnel Only" alongside Dixon, Jack, Vaughn and... Sloane. Meanwhile, the truth Sydney found out in Wittenberg endangers her relationship with Jack, and eventually she reveals the awful truth to Vaughn.

Dixon enlists Sydney to help him prove that Sloane is double-crossing the CIA and using APO to steal the Blackwell Index, a master blackmail list, and to reconstruct the Alliance. Sydney makes her way into Sloane's house so as to copy the encryption key from his secure phone and crack his calls. When Nadia finds her, she becomes disappointed in her sister. Meanwhile, Vaughn discovers something disturbing about his father when he visits his comatose uncle.

After a tactical group infiltrates the DSR and steals Rambaldi artifacts, CIA director Hayden Chase discovers that the alarms at the DSR were disabled from Nadia's computer, allowing the raid to happen, and shows up at the apartment to question her. Soon Sloane and Jack arrive and suspect that Sophia, who had access to the computer while she was living with Syd and Nadia, is Elena Derevko. They follow her trail to a dead Rambaldi follower, a stunning betrayal, and a presumed dead family member...

Rambaldi's catastrophic endgame begins to fall into place as a giant version of the Circumference/Mueller device is found floating over city in Russia, driving the citizens made. After a wounded Dixon reveals that Irina is alive, Sydney, Nadia, and Jack set off to find her. Irina had been captured, and then duplicated using Project Helix, in order to give the impression that she was dead.

Sydney and Nadia discover Irina is being held inside a camp in Tikal, safely in the clutches of Elena's army. Irina had apparently been working to counter Elena's organization, the Covenant, and actually PREVENT the Rambaldi endgame. Irina tells of a page she destroyed, a page that was key to Rambaldi's endgame. Under torture, she finally broke and recreated it for Elena. After a short respite, the transport turns towards Russia, and Sydney, Vaughn, Jack, Nadia, and Irina parachute down, towards Elena, Sloane, the Circumference....and destiny.