Sydney faces off with her mother, while Emily must decide whether to side with her husband or betray him.

Jack takes drastic measures to ensure that the NSC never finds out the truth about Sydney's murder of a Russian diplomat. But his actions place a heavy strain on Vaughn's marriage, as Lauren gets closer and closer to the truth about Sydney. Meanwhile, Sydney agrees to go on a mission with Sloane in order to thwart plans to obtain the operating system to a deadly weapon -- and she discovers an unlikely ally in the hunt for her missing two years.

After discovering the identity of the Rambaldi "Passenger," Sydney and Jack seek the aid of Sloane, to track the "Passenger" down. Meanwhile, after learning a secret about his father from Thomas Brill, Vaughn is kidnapped and tortured by Lauren and Sark, who are about to track "The Passenger" down themselves.

In an attempt to talk to Sydney, Katya Derevko deliberately poisons herself and is temporally taken out from her cell. Once Nadia tells her sister about this, Sydney visits her aunt to tell her to stay away from Nadia. However, Katya unsettles Sydney by telling her that someone framed her mother as a means of getting her killed. Sydney sets off in search of the truth behind this story. Meanwhile, Vaughn becomes a rogue agent by getting involved with the people who might know his father's whereabouts. In the end, he and Sydney find out that the man behind these two plots is no other than A. Sloane. However, things are not exactly as they seem to be.

Nadia's former caretaker, Sophia, has been severely beaten. She contacts Nadia and asks to meet her. Sloane is told by Sophia that she was beaten up, because someone is trying to track Nadia down, so he and Jack decide to tell their daughters the truth – Elena Derevko, the third and the most cruelest of the Derevko sisters, has been surveilling both Sydney and Nadia for a decade. Meanwhile, Jack's doctor advises him to tell Sydney about his illness.

Jack's illness has caused him to hallucinate about a cure. Sydney must recreate the time when Jack was working for the CIA and hid the only man who might be able to help him now. For this, Sydney must play her own mother. Meanwhile, Sophia moves in with Sydney and Nadia.

Sydney teams up with Renée - a fugitive on the CIA's most wanted list -- to track down the murderer of a close friend before the killer can strike again. Meanwhile, Jack enlists a reluctant new agent, Thomas Grace (Balthazar Getty), and Weiss struggles to decide whether or not to accept a promotion that would force him to leave his colleagues.

The entire APO gang is trapped inside the CIA offices and Weiss saves them. However, Weiss will not be returning to APO, he will just be helping the others on a mission to obtain information regarding Sydney.

Marshall reports to Jack that a microchip, found in Renée Rienne's body, is etched with the name 'Andre Micheaux'. Peyton tells Sloane that Sydney is being sent to Nepal to meet with someone regarding the chip. Sloane sends Anna, now Sydney's doppelgänger, to intercept. When Marshall discovers that the APO office is bugged, Jack frantically tries to reach Sydney to warn her before it is too late.