Sydney is trapped within the walls of Mangalev institute in Bucharest, Romania. Moments after finding SD-6 Agent Fisher with his throat slashed she is immobilized by a tranquilizer, and awakens in an electroshock tub. K-Directorate agent Dr. Kreshnik interrogates her, demanding to know if she received information from inpatient Martin Shepard, the FTL-trained assassin. Sydney assures she can extract the coordinates of Parkashoff's body from Shepard, as they have now established a basis for trust -- but only if Kreshnik allows her to live. K-Directorate grants her a stay of execution until nightfall.
She fights off Kreshnik, Ferroq and the orderlies, and with Shepard escapes to a remote CIA safehouse. The assassin's sight has been impaired by the FTL's tampering with his memory. When he looks at Sydney, he sees in black and white and cannot make a clear recollection.
As his memory returns, however, he reveals to her that he was Danny's killer, deprogrammed by SD-6 Agent McCullough... and Sydney tries harder than ever to forgive him, in the face of a killing for which Shepard was not truly responsible.
Vaughn contacts Jack to meet at a Chinese restaurant but Bristow is none too thrilled about this break in protocol. In turn, he confronts Vaughn for pulling his CIA file; Vaughn explains that Sydney wanted to see it because she suspects he used to have KGB affiliations.
At SD-6, Sloane informs Marshall that the virus found in the network was planted by SD-6 itself as part of a security drill. However, Sloane reveals in a face-off with Alain Christophe, elder statesman of SD-6 and the deadly Alliance, that SD-6 has set up a dummy server to catch the worm hacking into SD-6's mainframe. Christophe suspects a mole.
Will now has cold feet. He fears crossing a line with Sydney by defying her wishes to let go the details of Danny's murder, but after having pleaded earlier with his editor Litvack, he finds the story due for reassignment if he drops it.
Thanksgiving dinner is served at Sydney's, and Charlie proposes to Francie, which she accepts joyously. When Jack arrives, he tells Sydney that the FBI investigated him 20 years earlier, suspecting he was KGB, leading to the pursuit which forced his car off the road, killing her mother Laura.
Back at SD-6, Sloane has decoded the FTL communiqué, using Parkashoff's DNA, which reveals news that another Rambaldi artifact has been sent for analysis at Oxford's Department of Engineering. Sloane assigns Sydney to follow but Vaughn warns that Anna Espinosa was last sighted leaving Bucharest and may also be on the job.
Jack: Mr. Vaughn, you're young and you're eager, and I understand that. But one thing you're not, and this is something only time can provide really, is wise.
Vaughn: Sydney's life is worth the risk!
Jack: Not to Sydney! Taking them down is what gets her up in the morning. Or... did you think it was those meetings she has with you?
Will: She said her name was Kate Jones, but it was really Eloise Kurtz. She was my source in the Danny Hecht investigation. That means she was more than a source, she was involved somehow! She was trying to tell me something, and now she's dead!
Sydney: The irony is they never lied to me about what would happen if I told someone. It was the one thing they said that turned out to be true. Now I'm a double agent for the C.I.A. and I will be until SD-6 is gone.