On her first mission as a double agent, Sydney is sent to Moscow to retrieve some stolen files about nuclear bomb. Meanwhile, Will continues to grow obsessed with Danny's death and starts his own investigation even though Sydney asked him not to.

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.

Now nine months pregnant and on maternity leave, Sydney is surprised when her mother, Irina Derevko, shows up at her front door pretending to be a victim pursued by Prophet Five to get information on the whereabouts of 'The Horizon'. Jack, Sydney and Irina travel to Vancouver to an high-rise office building to steal the Horizon, only to get trapped on the upper floors when Peyton and hit team show up, forcing Jack to do battle with them alone as Sydney finally begins to go into labor with Irina as her labor coach. Elsewhere, while Dixon meets with Renee in Paris for information about The Horizon, back at APO, Rachel, Marshall and Tom agree to cover for Sloan when CIA Director Arthur Devilin arrives to monitor the APO records in the wake of the discovery of Prophet Five mole within the CIA.