Chuck finds himself in over his head when he receives an email from an old college buddy, who happens to be a rogue government agent. As Chuck gets sensitive information downloaded into his brain, he soon gets on the CIA's radar.
Tension rises when the doctor who is supposed to get the data from Chuck's mind is killed, pitting two government agents against each other as everyone tries to identify the killer.
With a promotion coming up for Chuck, he gets embroiled in an undercover mission as he tries to identify an elusive arms dealer at an art auction.
When an agent from Sarah's past appears to ask for help, Chuck finds himself in the middle of a scheme to steal a diamond before it could be used to fund terrorist attacks.
When Chuck runs amok of a Chinese spy trying to save her brother, his attempt to make amends lands him in the middle of a rescue mission.
When Chuck runs into a rogue government agent, he finds a kindred spirit in him as he observes the similarities between their situations, but he soon comes to regret his decision to help him.
Chuck is forced to confront his past when he returns to his alma mater to investigate the kidnapping of his former professor, only to find out more about Bryce Larkin and his complicity in getting Chuck expelled from school.
Chuck's double life becomes too taxing as he meets a girl that gains his interest. A plot from a poison specialist unexpectedly helps Chuck learn more information about his handlers.
As Chuck tries to make a choice between Lou and Sarah, external circumstances force his hand as a hidden secret is revealed about Lou. Sarah has to deal with her past, as well as her feelings for Chuck.
When Bryce makes a return, he enlists Chuck's help to prove his innocence. Chuck's world turns upside down as his relationship with Sarah appears doomed.
In an attempt to bust a counterfeiter, Chuck has to counter Sarah and Casey's doubts about his ability to be partial and make sound judgments.
When Chuck runs into a former sweetheart of Casey's during a mission, he pesters Casey into making a move before she gets married off.
After Buy More is raided, Chuck learns that a bug has been planted inside the store, leaving the CIA to take drastic measures to protect him until they could find the spy.