Two new characters are introduced, both of whom want to take the Intersect. One is a beautiful, young female enemy agent that works in the Pita Palace next to the Buy More, and the other is a handsome CIA agent who is posing as an undercover police detective investigating a theft at the Buy More who wants to take Chuck into his custody. The former quickly blows Chuck's cover, while the latter kidnaps him and makes him vanish from his former life.

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.

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.

The episode begins with a flashback to the year 2004, where John Casey is involved with a female Russian named Ilsa, who claims she is a photo journalist. Later, in present day, Ilsa returns with a fiancé, named Victor Federov. Things get complicated when it is revealed that Ilsa is a French spy.

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.

After his intuition is wrong while working on a stakeout, Chuck feels morally obligated to make things right, even when both Sarah and Casey refuse to help with Chuck's new mission. Meanwhile, Morgan has to participate in a sales competition that could decide his fate at Buy More.

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.

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.

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's latest mission has him raiding a Malibu mansion to grab a million dollar diamond being used to fund terrorism. Tagging along is an attractive but less-than-trustworthy DEA agent.

While coping with the realization that Sarah still has feelings for Bryce, Chuck must assume his toughest cover yet by going on a mission as Sarah's husband. The team must foil the plot of a politically connected counterfeiter, who may be endangering the lives of Anna, Morgan and Anna's parents. Both Morgan and Anna also find themselves in the cross hairs.