Chuck Bartowski is an average computer geek until files of government secrets are downloaded into his brain. He is soon scouted by the CIA and NSA to act in place of their computer.

Returning to Stanford, the University that expelled him, Chuck has to help a former professor who is a government agent being hunted for a sensitive top-secret file he has in his possession. At the same time, Chuck learns much about himself and about the death of his friend Bryce Larkin.

Not all of Sarah's feelings for Chuck may have been a cover, as she finds out, when Chuck begins to date Lou, a sandwich maker. When things couldn't get even more complicated, Lou turns out to be part of a smuggling ring.

Chuck discovers that his former roommate and old nemesis, Bryce Larkin, is still alive, and that a renegade group within the CIA is after the Intersect. Chuck then has to balance helping Bryce return to the legitimate CIA, with the year's busiest shopping day at the Buy More.

Chuck needs to go undercover to seduce a woman named Sasha Banachek, so an old school spy named Roan Montgomery is assigned as his mentor. Meanwhile, Captain Awesome finds himself in need of some relationship advice, and and turns to Morgan, and Lester faces his first problems as assistant manager.

Bryce Larkin returns to town with news about Fulcrum. They have hired a wealthy software magnate named Von Hayes to decrypt information on a stolen chip containing a refresh to the Intersect with highly classified information. Bryce and Sarah have to pose as a married couple at Von Hayes' dining party to steal back the chip, while Chuck has to pose as a waiter. Meanwhile, Morgan has an encounter with the Mighty Jocks at the Buy More.

Ellie's big day finally arrives and Chuck must save her life and her wedding from being ruined by Ted Roark and FULCRUM.