Five months later. Sydney quits the CIA and joins a Black Ops unit called "Authorized Personnel Only" alongside Dixon, Jack, Vaughn and... Sloane whom for limited immunity is co-operating with the APO. Meanwhile, the truth Sydney found out in Wittenberg endangers her relationship with Jack, and eventually she reveals the awful truth to Vaughn: about her father having Irina murdered over a year earlier.

Dixon secretly 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 of Twelve. Sydney makes her way into Sloane's house so as to copy the encryption key from his secure phone and crack his phone calls. When Nadia finds Sydney snooping around Sloane's computer, she doesn't tell him, but becomes disappointed in her sister and begins to lose trust with Sydney. Meanwhile, Vaughn discovers something disturbing about his late father when he visits his comatose, dying uncle who makes a remark about seeing his father - recently.

After a tactical group infiltrates the DSR and steals all the Rambaldi artifacts, CIA director Hayden Chase discovers that the alarms at the DSR were disabled from Nadia's computer, allowing the raid to happen. Mrs. Chase 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 Sydney and Nadia, is in fact Elena Derevko. They follow her trail to a dead Rambaldi follower, a stunning betrayal, and a presumed dead family member when in a surprising twist, Sydney and Nadia learn that Irina Derevko is in fact alive.

Rambaldi's catastrophic endgame begins to fall into place as a giant red ball version of the Circumference/Mueller device is found floating over a large city in Russia, driving the citizens mad with violence. After a wounded Dixon reveals that Irina is alive, Sydney, Nadia, and Jack set off to find her. It turns out that 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 being held inside a camp in Tikal, safely in the clutches of Elena's private army. Irina had apparently been working to counter Elena's organization, the Covenant, and actually PREVENT the Rambaldi endgame. Irina is taken to APO and tells them 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, Sydney, Vaughn, Jack, Nadia, and Irina board a plane parachute down, towards Elena, Sloane, the Circumference....and destiny.