Season 2: Episode 1 - "The Enemy Walks In"
 

Sydney recounts her most recent mission to a CIA psychiatrist: Tied to a chair somewhere in Taipei, Khasinau introduces her to "The Man" — who is actually her mother, Irina Derevko. Saying that she should have killed Sydney when she was born, Irina shoots her in the shoulder to make a point, then exits. Sydney, however, escapes by smashing the chair against a water valve.

She rendezvous with Jack, who has rescued a badly beaten Will, and explains what happened. She and Jack then reveal the truth about themselves and SD-6 to their panicking friend.

Jack enacts a cover-up: He tells Sloane that he gave Sydney the "Freelancer" call sign because he didn't trust Sloane and that Will's kidnapping led them to Khasinau, who's organization is now fractured. He pleges loyalty to Sloane and convinces him to spare Will's life. As a consequence, Dixon apologizes to Sydney for questioning her loyalty.

Sloane then sends Sydney to the French estate known as Le Petite Rose to plant a phone bug in the office of Jean Luc Rave, a Khasinau cohort and member of the French National Assembly. Sydney gives Marshall's bug to Agent Weiss, who inserts a delayed transmitter that controls what SD-6 will hear.

Having parachuted onto the estate, Sydney finds an unconscious Vaughn about to be butchered by Khasinau. She revives him with an adrenaline shot to the heart. He explains that he used a screwdriver to open a grate, which allowed him to escape the flooded room. When the psychiatrist questions her about Vaughn, she gets defensive.

Meanwhile, Jack ensures Will's safety by drugging him and placing him at the scene of a drug bust. Under media scrutiny, Will claims his story about SD-6 is a lie. His reputation is ruined, but his life is saved.

The CIA sends a team, including Sydney, to Barcelona, based on info gleaned from the bug. The "Bible," an operations manual for the Khasinau/Irina cartel that had been in Taipei, is to be given to Khasinau on a Barcelona pier. SD-6 is unaware. But in an ambush, Irina shoots Weiss and the players scatter. Sydney trails Khasinau, who has the Bible, to a warehouse where they're confronted by Irina. Irina kills Khasinau and takes the Bible. Before leaving, she tells Sydney, "Truth takes time."

Back home, Sydney tells Will that she's glad she doesn't have to lie to him anymore and then leaves to eulogize Emily Sloane. At the CIA headquarters, Irina comes in from the cold and surrenders.