When former SD-6 agent McKenas Cole with his crew of bandits take over SD-6, Sydney has to forget her previous plan about quitting the agency and has to focus on her mission with Jack to save their colleagues. In the meantime, as he was about to quit his work on a story, Will Tippin gets an unexpected push to continue from the third party.

Vaughn disobeys the CIA in order to infiltrate SD-6 when he receives a desperate plea for help from Dixon. At SD-6, Cole continues his vendetta against Sloane and his search for device in possession of SD-6. Elsewhere, Will continues his work on story.

In this episode, Sydney finally learns the shocking truth about her missing two years from an unlikely source: FBI Special Officer Kendall. Kendall whisks her away and talks to her from the privacy of an airborne 757 jet. According to Kendall, Sydney was captured by the Covenant after her fight with Francie/Allison, held captive in Russia for over a year and brainwashed to become an assassin. But Sydney only pretended to be brainwashed and contacted Kendall who became her contact and handler, thus giving him information about the Covenant and about their quest for Rambaldi artifacts. Sydney also staged the murder of Andrian Lazarey, and then deliberately had her memory erased to prevent the Covenant from knowing about secrets she had learned about Rambaldi's findings.

Sydney and Vaughn are sent to retrieve the Doleac Agenda to gain an advantage over The Covenant. For this, Sydney and Weiss must convince rogue security systems designer Toni Cummings to help the CIA break into a Lethal Response System. Meanwhile, Sark approaches an unlikely ally, that of Lauren Reed, to kill the Covenant's six cell leaders in order to take control of Covenant for themselves.