In season three, Chuck finally has the potential to become a real agent. There's just one problem — his emotions. Can Chuck keep them in check as he assumes his new role as the Intersect 2.0? His handlers, Sarah Walker and John Casey, will still be there to protect him, but they also must help him become the agent he is destined to be.

The second season continues to focus on Chuck's constant struggle to keep his spy life and real life apart as he becomes more accustomed to being a spy. More background on the Intersect project is revealed. Fulcrum, a hostile espionage organization that covets the Intersect, is featured more heavily as the season's main antagonist. Chuck and Sarah continue to grow closer, complicating their asset-handler relationship.

The first season of Chuck introduced the series' main characters and established the general plot of the title character, Chuck Bartowski, having to adapt to his new life as a spy after the only remaining copy of the U.S. government's spy secrets are embedded into his brain. He is forced to juggle his responsibilities as a spy and the supervisor of a technical support team, called the "Nerd Herd", at his local Buy More store. Having become the most important asset of the U.S. government, Chuck is under the constant surveillance of his CIA handler, Sarah Walker, and NSA agent John Casey, who remind him that he cannot reveal his spy life to his sister Ellie, nor his best friend Morgan Grimes.