Sydney is sent to Greece to retrieve information about new weapons that are being produced by a young tycoon. Meanwhile, Vaughn plans to report Jack for his apparent involvement in murders of many CIA agents and by doing so, he crushes Sydney's newly found admiration for her father.

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.

Department of Special Research gained interest in Sydney's role involving the page 47 and they began their own investigation regarding it. To save herself, Sydney needs to steal 500 year old Rambaldi codes from Vatican to decipher Rambaldi's prophecy. Meanwhile. Sloane gets suspicious that one of the Alliance's members switched sides and is now working with The Man.

Francie is having a rat problem in her house and gives an inspiring speech about catching them which gives Sydney idea how to catch Khasinau. She and Vaughn set up fake transaction for a Rambaldi artifact with Sark, but their job is compromised when Sloane sends SD-6 agents to steal the presumed second vial. Meanwhile, Will learns the truth about his kidnapping and Jack Bristow has no option but to help him.

Sloane must take a difficult decision in order to get to the Alliance's council. After being captured by Sark, Tippin is tortured by a Taiwanese would-be dentist to extract secrets. Sydney, who has to beware her colleague Dixon, assist her father trying to save Tippin. However, after losing Vaughn when the lab exploded, she is in for a surprise...

Sydney's fury at Jack's present betrayal and past sins leads her father to a desperate act to prove his love for her. Meanwhile, Vaughn - after enlisting Will in a seemingly benign CIA request - learns that a mission He and Sydney engaged in could have disastrous consequences for their health.

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.