Sydney's search for her past leads to an imprisoned Sark, but their Q&A is cut short when he becomes the ransom for a pair of abducted CIA scientists by the Covenant, whose kidnappers may be tied to the murder of his father. Meanwhile, Jack contacts an old friend of sorts for info on Sloane's new world-peace project in Switzerland. Also, Vaughn makes a decision about his future as an operative for the CIA.

In this episode, Sydney finally learns the shocking truth about her missing two years from an unlikely source: FBI Special Officer Kendall. Kendall whisks her away and talks to her from the privacy of an airborne 757 jet. According to Kendall, Sydney was captured by the Covenant after her fight with Francie/Allison, held captive in Russia for over a year and brainwashed to become an assassin. But Sydney only pretended to be brainwashed and contacted Kendall who became her contact and handler, thus giving him information about the Covenant and about their quest for Rambaldi artifacts. Sydney also staged the murder of Andrian Lazarey, and then deliberately had her memory erased to prevent the Covenant from knowing about secrets she had learned about Rambaldi's findings.