Sydney's cover in SD-6 is put in danger after smuggling a wrong biotech engineer into SD-6 from her mission in Berlin. Meanwhile, Will's investigation into Danny's murder leads him to a woman named Kate Jones, who may have information about the killing. Sydney's starts to doubt where her father's true allegiances lie.

After making a shocking discovery of a severed human hand in the desert that belonged to Lazarey, the Russian diplomat she murdered while working as a brainwashed assassin for the Covenant, and who may in fact be alive, Sydney agrees to submit to an experimental procedure conducted by an eccentric doctor, named Dr. Brezzel, designed to retrieve her lost memories. But while Jack and Vaughn look on, Sydney's mind proves surprisingly resistant to letting her remember her missing time... and the process of recovering it could end up killing her. Meanwhile, Lauren makes a great sacrifice of allowing herself to get tortured and beaten up in order to make her alibi believable to Lindsey after helping breaking Sydney out of NSC custody. Also Sloane finds himself boxed in by an unlikely enemy, that of Mr. Lindsey, who wants to see Sydney Bristow eliminated permanently.

Sydney attempts to rescue Dixon's kids after they are kidnapped by Sark. Meanwhile, Lauren's status as a double agent for the CIA and the Covenant is put to the test when she learns that she has to work with her father; a wealthy U.S. Senator. When Laura's position is compromised, she and Sark decide to frame Sloane for being the CIA mole.