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.

As Chuck is beginning to adapt to his new life as a spy, a doctor who could possibly "cure" Chuck is murdered. Chuck then begins a high-speed fight for his life, all while trying to decide which of his two new colleagues might be out to get him. Meanwhile, Chuck's sister Ellie invites Sarah to dinner to meet the family.

Chuck needs the help of Morgan and the Nerd Herd to prove that he is ready to become the store's assistant manager. Sarah and John assign Chuck his first undercover spy mission to foil a terrorism plot.

In this Halloween episode Chuck meets a Federal agent just like him: A computer whiz whose brain is important to national security. However, Chuck soon has a personal dilemma arise when he has to decide whether or not to turn the man over to Sarah and Casey or to help him escape his handlers.

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.

Chuck must learn to balance a real love life with his cover love life when he meets a charming young woman by the name of Lou. At the same time, his relationship with Sarah gets interesting when the duo must explain their sexual relations with Ellie and Captain Awesome on a double date. Meanwhile, there is trouble when someone is using truth poison in order to retrieve codes for nuclear facilities.