Chuck is a computer geek who gets a computer full of information zapped into his brain...information that contains secrets that the federal government desperately needs to keep in Chuck's head...and keep Chuck, himself, intact. In the opener Chuck meets a woman who agrees to go on a date with him, but she's one of the government agents who's interested more in his head than his body.
The Government wants to verify the secrets are inside Chuck's head. So they send a doctor who programmed the Intersect system to examine Chuck. When the doctor's car explodes. There's evidence one of the agencies was involved, leaving Chuck unsure whom to trust.
Chuck spots a man wanted by the government. He finds out the man worked for the government, and just desired a new life. Soon he has Chuck doubting his handlers. Chuck has to interview for Assistant Manager.
After breaking up with Sarah, Chuck starts dating Lou. When Chuck flashes on Lou's ex-boyfriend. He's conflicted between his current love interest and his duties. The agents intercept the shipment, and find something totally unexpected.
Bryce is alive. When he's revived the only person he wants to talk to is Chuck. He tells Chuck he wasn't rogue, and the people he was working for are after the Intersect. It's up to Team Chuck to bring Bryce in, and protect Bryce and Chuck.
Chuck flashes on a counterfeit bill on a philanthropists yacht. Team Chuck goes undercover to determine what he's up to. Chuck's inexperience causes problems. Morgan meets Anna's parents. Casey receives major news that will affect the entire Team.
Chuck finds a bug in the Buy More, and gives it to Casey. Neither of his handlers planted that particular bug. Fearing Chuck's cover has been exposed, the government prepares to bring him in. While the agents try to find the culprit, Chuck tries to find an engagement ring Devon asked him to hold until Devon can propose to Ellie.