Chuck receives an email from Bryce, an old roommate and friend who is a rogue government agent. The email contains government secrets which are downloaded into his brain. The CIA and the NSA both want to get the data back, so they send their agents Sarah and John to retrieve the data.
When a doctor who is brought in to recover the data from Chuck's mind is killed, John and Sarah turn against each other. Chuck eventually believes Sarah to be the killer, which causes a tense situation when the two of them attend a dinner hosted by his sister. It turns out that the doctor faked his death and kidnaps Sarah in order to force her to tell him where Chuck is because he wants to sell the secrets. While trying to rescue her, Chuck is captured. After a struggle inside a helicopter, Chuck finds himself forced to pilot the vehicle to safety.
Chuck's visions tell him that an arms dealer known only as "La Ciudad" ("The City" in Spanish), whose appearance is unknown, will be present at an art auction. Chuck is therefore forced to infiltrate the party with Sarah to try and identify La Ciudad. Chuck ends up dancing the Tango with a seductive Latin woman, Malena, who turns out to be La Ciudad.
When a diamond hidden in Malibu is used to fund terrorists, Chuck has to help steal it back. Complicating things further is the appearance of Carina, a DEA agent friend of Sarah's, who tries to help in her own way.
Chuck faces his first moral dilemma as a spy. When Chuck sabotages the mission of a Chinese spy who is trying to save her kidnapped brother, Sarah and Casey refuse to help him fix his mistake. However, the spy forces Chuck to help her get him back, and Sarah and Casey help too, on the condition that she defects from her spy organization. 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, only later to find out it was a ploy to make the sales team work harder. It is also revealed that Chuck's mother left them and his father was never around, so he and his sister celebrate their mutual support with an annual party. This year they were going to have shrimp for the party, but Chuck was unable to attend due to his spy troubles.
Chuck accidentally runs into a runaway 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 faces a predicament: either try turn this agent in to Sarah and Casey or help him escape his handlers. Meanwhile, Halloween, a holiday that means a lot to Chuck and Morgan as buddies, proves to be a little different this year as Morgan feels that Chuck is neglecting their childhood and friendship. They reconciliate and wear a two-man Sandworm costume to the party. Also, Chuck gets an interview for the assistant manager position, but is forced to miss it.
Chuck has to return to Stanford University, the institute that expelled him, on homecoming weekend to help a former professor, who, as Chuck finds out, is also a government operative being hunted for a sensitive top-secret file. Chuck must use his past experiences to find the Professor's hidden secret, while also discovering shocking secrets about his own life. More importantly, Chuck discovers the truth about his former friend Bryce Larkin and why Bryce had Chuck kicked out of Stanford. Meanwhile, Morgan has problems with the new assistant manager at Buy More.
Chuck battles with his cover love life and real love life when he meets a girl named Lou, who seems interested in the real Chuck. On the other hand, his relationship with Sarah (Yvonne Strahovski) heats up as they go on a double date with Ellie (Sarah Lancaster) and Captain Awesome (Ryan McPartlin) and try to explain their sex life. Meanwhile, a poison specialist is trying to obtain codes to nuclear facilities and is using a "truth" poison to help get his answers. After all are exposed to the truth, Chuck soon discovers a lot about his partners.
Chuck starts dating Lou, a sandwich-maker, and things seem to be going really well, which incites some jealousy on behalf of Chuck's "ex-girlfriend" Sarah, who discovers that her feelings for Chuck are more than just a cover. Things get complicated when Lou is discovered to be part of a smuggling group; although she believed it was smuggling only meats such as salamis, when they also smuggled weapons. Chuck and Sarah have to defuse a bomb, fail and, expecting to die in the detonation, the pair share a passionate kiss as the timer runs out. Then share an awkward moment when the "bomb" turns out to be something else entirely. Chuck leaves Lou and tries to start a genuine relationship with Sarah; however, Sarah finds out that her former lover Bryce Larkin is still alive. Meanwhile, Morgan starts developing a new relationship with Anna, another employee at Buy More.
It's Thanksgiving and Chuck's nemesis, Bryce Larkin, returns after being thought dead earlier. Bryce needs Chuck to help prove to Sarah, Casey and the rest of the CIA that he is not a rogue agent. Upon seeing Bryce and Sarah back together, former partners and lovers, Chuck becomes jealous and doubts any future with Sarah. Meanwhile, Buy More is prepping for the biggest shopping day of the year and Morgan is left in charge.
Still licking his wounds after realizing Sarah continues to have feelings for Bryce, Chuck must assume the cover of being Sarah’s boyfriend on a mission to foil a politically connected counterfeiter and yachtsman. Emotions and sea legs are tested when Chuck, Sarah and Casey have to head to the marina to stop a plot that also puts an unwitting Morgan and Anna squarely in the crosshairs. Meanwhile, it’s time for the annual Buy More holiday party, but the party comes with lots of rules from Big Mike.
Chuck discovers that many Russian arms dealers are secretly meeting in Los Angeles. One particular Russian woman catches his attention, and he flashes on her as being Agent Casey’s ex-girlfriend. Chuck grows very intrigued and begins to pester Casey about their history. After learning this woman is set to marry one of the Russian arms dealers, Chuck insists that Casey fights for his woman. Will Casey fight for his true love without compromising his identity? Meanwhile, Captain Awesome and Ellie reach a tough point in their relationship.
Captain Awesome asks Chuck if he can have Ellie’s hand in marriage, and then insists Chuck holds on to the ring until he plans it all out. Chuck decides to lock it in his Buy-More locker, and returns the next day to discover everything had been stolen from the store. Meanwhile, Agent Casey and Agent Walker discover that the someone has been spying on them in hopes of discovering “the intersect.” With Chuck’s identity and life on the line, NSA has no other option than to relocate Chuck into a permanent holding cell. Will Chuck lose his family and friends forever?
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