Chuck Bartowski is a computer geek that gets catapulted into a new career as the government's most vital secret agent. When Chuck opens an e-mail subliminally encoded with government secrets, he unwittingly downloads an entire server of sensitive data into his brain.
Chuck Bartowski is still trying to come to grips with his newly adopted life as a spy, tension builds between his recently appointed partners Sarah Walker and John Casey. When a doctor who seems to have a solution to Chuck's problem is killed, Casey and Walker turn the blame at one another. Both agents persistently try to convince Chuck that the other one is responsible and now it is up to Chuck to decide which one to trust.
Chuck Bartowski is finding out that living two separate lives is not going to come easy. After being challenged by his boss at Buy More, Chuck needs the help of his best friend Morgan and the Nerd Herd, to prove that he is up to the task and ready to become assistant manager. Meanwhile, Sarah and John force Chuck to go undercover for his first real spy mission.
Chuck decides to help Sarah and her colleague when he finds out that a million-dollar diamond hidden in a Malibu mansion is being used to help fund terrorists. Morgan tries to get Chuck to set him up with Sarah's new friend. Chuck is finding out that Sarah's job of living a double life, which she is all too good at, is preventing him from getting to know who she really is.
Chuck faces his first moral dilemma as a spy. When agents Sarah and Casey refuse to help an unauthorized mission that is taking place in Chinatown by a top Chinese spy, Chuck is faced with a tough decision. He must decide whether to follow orders or do what he believes is right. Meanwhile, Morgan is caught in a dilemma of his own when Buy More forces him into a sales competition that could cost him his job.
Chuck accidentally runs into a fellow government agent who seems to be living a similar life. It turns out this agent is a gadget whiz, whose brain makes him a national security asset and a dangerous liability, much like Chuck.
Chuck returns to Stanford University, the institute that expelled him, on homecoming weekend to help a former professor. Chuck finds out that his former professor is also a government operative who is being hunted for a sensitive top-secret file.
Chuck battles with his cover love life and real love life when he meets a very pretty girl named Lou, who seems interested in the real Chuck. On the other hand, his relationship with Sarah heats up as they go on a double date with Ellie and Captain Awesome and try to explain their sex life.
Chuck starts dating Lou, a sandwich maker, and things seem to be going really well. This incites some jealousy on the behalf of Chuck's "ex-girlfriend," Sarah, as she may be discovering that her feelings were not all just a cover.
It's Thanksgiving and Chuck's nemesis, Bryce Larkin, returns to his life after being ruled dead earlier in Chuck's life. Secret internal committees trying to destroy the "intersect," now better known as Chuck's brain, saved Bryce in hopes he would be able to help them locate it.
Still licking his wounds after realizing Sarah continues to have feelings for Bryce, Chuck must assume the cover of being Sarah's husband on a mission to foil a politically connected counterfeiter and yachtsman.
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 fiancee named Victor Federov. Things get complicated when it is revealed that Ilsa is a French spy.
Casey and Sarah discover that the CIA has been spying on them and are forced to relocate Chuck.