In a comfortably appointed 747, Sydney poses as a call girl and models lingerie for an unnamed fat man. She gets close to him, surprising him with a choke hold and demands to know the location of Server 47. He tells her, and she knocks him and downloads data from the terminal. She searches the plane for a parachute and fends off a guard — but the fat man appears brandishing a gun and fires at Syd …

At the CIA, Vaughn pulls Sydney aside and says that it isn't working between them because he's going crazy with passion and worry for her. She agrees but they rationalize their chemistry is helping bring down SD-6. Weiss interrupts and they end the conversation. Kendall reveals that Sloane is MIA and has been replaced as head of SD-6 by Anthony Geiger. Syd and Jack's new mission is to get close to him.

At SD-6, Sydney introduces herself to Geiger, professes loyalty and, under his questioning, tells him that she felt it was her fault that Sloane had Danny killed. Later Sark tells her that he's nervous about Geiger, who has looked into Sloane's secret files on Server 47. Syd then tells Jack that this mysterious server could have crucial information about the Alliance that could make them vulnerable.

Vaughn locates the Server 47 — it's on a continuously airborne 747 that lands only to refuel and is guarded by a man named Macor (the fat man). As payment for spending his life on the jet, he's supplied with an unlimited number of call girls. Syd's mission is to gain access to the server in the main cabin by playing a high-priced hooker.Vaughn and Weiss observe Sydney's conduct via a monitor from a cargo plane flying at a lower altitude. They watch with disbelief as Macor's shot misses and as Syd picks up a gun and fires — puncturing the plane's hull and depressurizing the cabin. Macor is sucked out and drawn into the jet engine. Struggling against the vacuum, Sydney manages to find a parachute and jumps to safety.

In L.A., Will tells Francie that he must quit her restaurant because he got a job as a travel writer. She's genuinely happy for him and an innocent kiss turns romantic. Later on, they tell Sydney.

Kendall is reluctant to move on the info downloaded from Server 47 because the risk is too great if it's incorrect. Sydney suggests they verify the security code at the SD-6 computers with what's in the new info. If it matches, then the info is accurate.

Meanwhile, Geiger notices a strange email that Sloane had written and runs a program that tracks keystrokes. The email reveals that Sloane knew that Jack and Syd were double agents working against SD-6!Geiger confronts Jack. Jack calls Syd and tells her to come down to SD-6, but to take surface streets because the highway is jammed — a coded phrase meaning he's been compromised. Geiger tortures Jack with electrocution, hoping to find out who Jack's working for.

Sydney is frantic because she can't help Jack and knows Kendall will think a rescue is too risky. She tells Will and Francie to leave town because someone is looking for her. She then meets with Dixon and reveals to him the truth about SD-6 and her role as a double-agent. She asks him to hack into SD-6's innermost server and make visible to the CIA the code that will verify their info. Dixon is dubious but acquiesces. When the CIA receives the code, Kendall orders a global assault on all Alliance and SD cells.

A CIA team overruns SD-6. Sydney finds Jack just in time and shoots Geiger. As the CIA gains control of the facility, Sydney and Vaughn see each other amidst the carnage and kiss passionately!

Later Sark, who has escaped unharmed, phones Sloane and informs him that Phase One is complete. A pleased Sloane asks him to check in on their "new asset." Sark phones … Francie. But it's a double. She's murdered the real Francie, who lies on the floor with a bullet to her head!