Sydney and Vaughn wake up together. During their bedroom chatter, Syd mentions that it's her graduation day and discusses her desire to leave the agency. Kendall later refuses Sydney's resignation, adding that as a civilian she would no longer be able to see her mother. Irina, hoping to push her daughter away from the CIA, says she will refuse to see her if Syd stays with the agency.

At the Long Beach Aquarium, Sark kidnaps Neil Caplan, a Cal Tech mathmetician, along with his wife and child. They're taken to Switzerland, where Sloane shows Caplan the Rambaldi manuscript and explains his 30-year-search for artifacts.

As Syd prepares for her graduation, Sloane calls, ostensibly to congratulate her. He admits he knew she and Jack were double-agents and that he used them to free himself of The Alliance. He warns her not to get in his way. At the CIA, Kendall briefs Syd on Sloane's kidnapping of Caplan, whose knowledge of Knot Theory — how geometric objects fit together — would enable Sloane to build a weapon out of the Rambaldi artifacts. Syd wearily realizes the battle against evil is eternal, and rethinks her resignation.

Sydney tells Dixon that he's been cleared, and offers him a CIA job. Dixon, however, feels manipulated by Syd and never wants to see her again. He goes home to his wife and confesses his life of deception. Despite his vow to be honest with her in the future, she later says that she'll leave him if he joins the CIA.
Marshall, on the other hand, has already adapted to the CIA and has found a Sloane associate — Holden Gemler, a cybernetics specialist in Van Nuys. Jack discovers Gemler's body, sans one eye, during a search. Marshall reveals that the eye is actually a tracking device and they deduce that Sloane hired Gemler to deactivate his own Alliance-implanted tracking device. Marshall accesses the memory in Gemler's eye, which shows Sloane killing Gemler and mentioning a chartered C-123 cargo plane from Shipman.

Shipman is a smuggler-operated airfield in the Mojave Desert. With Vaughn posing as an arms dealer, Syd sneaks in and downloads the plane's data recorder, which will reveal Sloane's final destination as Switzerland. Syd repels an attacker, sending him into the plane's propeller.

With Caplan agreeing to help Sloane in order to save his family, Sloane plans to break into a Zurich bank that holds Caplan's invention, a magnetometer, which can measure magnetic fields and fit the Rambaldi pieces together perfectly. Sloane talks to Emily, telling her that their Tuscan villa will be ready in a few more days.

In Switzerland, Vaughn contacts a mercenary employed by Sloane and nearly sets him afire before he reveals the location of Caplan's wife and child. With the family rescued, Syd has Marshall triangulate the calls from a cell phone she found on a kidnapper and finds that they originate from the Zurich bank. Syd and Vaughn race through the streets to get there in time.
At the bank, Sloane, who has changed his appearance to that of an elderly man, gains access to the vaults under the pretext of making a $50 million deposit. He shoots the bank manager and finds the magnetometer. Syd and Vaughn arrive as Sloane and his team are leaving. The standoff is broken when Sloane says he has rigged the lower level with enough C-4 to destroy a city block and if he doesn't exit in 30 seconds, an off-site team will detonate it. Sydney and Vaughn toss their guns to the ground. Sloane throws Sydney a set of keys, telling her that she will drive him out.