Sloane temporarily steps down as director of his APO task force and gives Jack full authority over the next assignment, which involves Anna Espinosa, the former K-Directorate assassin and Sydney's old foe into racing her to go after stolen classified documents. However, Anna turns the tables on APO when she captures Nadia and forces Sydney to do her bidding. During this time, Sydney tells Nadia about the Rambaldi's prophecy which dictates that "two sisters will fight, and only one will survive." Meanwhile, Vaughn visits the imprisoned Sark and tries to trick him into helping them to catch Anna.

After escaping from Peyton and her henchmen, and learning she's on a freighter at sea, Sydney goes to the communications room and sends a message to APO routed through the CIA to her whereabouts. Unbeknownst to her, the message is intercepted by a mole at the CIA working for Prophet Five, although APO was able to obtain a piece of the transmission. Wanting to retrieve Sydney, the APO team, Rachel, Tom, Dixon, and Marshall attempt to break into a secured server room located at Langley with the goal of obtaining the remaining part of the transmission. Problems arise, however, when APO is forced to take the hard drive, which triggers an alarm. They manage to escape the situation thanks to former APO agent Eric Weiss who aids them in sneaking past the guards. Although the transmission on the hard drive is corrupted, APO is able to learn who corrupted it. Jack sets a meeting up with the division heads of the CIA and is quickly able to identify the mole. Meanwhile, Tom is revealed to have another agenda when he obtains information about a certain Allan Korman, who was a former German assassin now in a witness relocation program, and who murdered Tom's wife many years earlier.