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.
As the upgraded Intersect, Chuck trains to become a full-fledged spy but hits rock bottom when he flunks out of spy school and loses Sarah in the process. Meanwhile, Morgan comes home from Benihana School to help Chuck get over Sarah.
Chuck gets a new mission when Sarah's best friend Carina comes through town with her fiancé Karl. Things get complicated when Chuck wants to hash out his and Sarah's relationship problems while they're on the mission. Meanwhile, Morgan finds himself in trouble when he lies to Jeff and Lester.
Chuck must use his relationship with Awesome to protect a visiting dictator, Premier Goya, who is the target of an assassination. While Awesome is excited about the prospect of being a spy, Chuck is more concerned about Awesome and Ellie's safety.
When Awesome is mistaken for a super spy by the evil Sydney Price, Chuck must become his handler and show him the spy ropes. While on a mission for The Ring, they meet the mysterious Daniel Shaw. Meanwhile, Morgan gets promoted to assistant manager and must deal with Jeff and Lester's latest hijinks.
CIA agent Daniel Shaw assigns Chuck to his first solo mission in Paris, ignoring Sarah and Casey’s wishes. During the flight to France, Chuck befriends Hannah and flashes on another passenger the imposing Hugo Panzer. Meanwhile, Casey helps Morgan battle Jeff and Lester for control of the Buy More.
Chuck juggles his two lives as he trains new Nerd Herder Hannah and gets his very own asset who is caught up with The Ring. Chuck thinks he can handle his asset all on his own but Sarah and Casey feel the need to intercede. Meanwhile, Awesome must lie to Ellie when she starts to ask questions about Chuck and Morgan, Jeff and Lester do some recon work to learn more about Hannah.
Chuck and Hannah unexpectedly become part of agent Daniel Shaw's latest mission. Much to Sarah's chagrin, she gets paired with Shaw, who seems to be trying to get close to her. Meanwhile, Morgan and Ellie continue their mission to get to the bottom of Chuck's secretive and strange behavior.
Chuck promises to cook dinner for Hannah, Ellie and Awesome but must first assume the identity of the world's most dangerous assassin for his latest mission. Meanwhile, Sarah is determined to keep her relationship with Shaw strictly professional.
Chuck feels like his life is falling apart when he can't flash and gets left behind for a mission. While Shaw, Sarah and Casey go on without him, Chuck finds himself in a sticky situation back at the base.
Casey carries out a side mission for his old commanding officer James Keller that leads to him committing treason. When Chuck learns the dark truth about Col. Keller, he and Sarah set out to break Casey out of jail and clear his name. Meanwhile, Awesome's plan to keep Ellie out of danger gets more difficult when she gets her dream fellowship.
Chuck learns that his latest solo mission will be a final test to see if he is ready to be a spy. Chuck needs to put everything he has learned into action to avoid going back to his old life while Sarah and Shaw observe his every move.
Chuck has his pick of the best CIA agents for an undercover operation, but he has only one girl in mind for the job, Sarah. Casey, Morgan and Awesome team up to help Chuck win her back.
Chuck, Sarah and Shaw reunite to find the Ring operative behind the death of Shaw's wife. Sarah has faith that Shaw is ready for the mission but Chuck is worried about his emotional stability. Meanwhile, Morgan considers leaving the Buy More.
While in Europe, Sarah and Chuck realize they’re traveling on a train with Spanish spies. Even though they’re all alone, they decide to take on these rogue agents. Of course, this impromptu mission doesn’t go smoothly. Meanwhile, Beckman orders her newest “unlikely” spy team – John Casey and Morgan Grimes – to track down the missing couple.
Chuck and Sarah are assigned to train under Craig and Laura Turner, a married CIA team who, despite their impeccable record, hate one another. The Turners' stormy relationship forces Chuck and Sarah to wonder if they're doomed with the same fate. Meanwhile, Casey must train the newest member of the team Morgan.
Chuck struggles with disturbing dreams and now he believes his most recent dream predicts danger for a visiting head of state. General Beckman however, is unconvinced and assigns Chuck to meet with a CIA psychiatrist Dr. Leo Dreyfus. Meanwhile, Ellie gets surprising news and Anna returns to the Buy More to talk to Morgan.
After his last dream, Chuck asks Morgan to help him on a side mission. Their investigation becomes complicated when Stephen J. Bartowski returns and learns that Chuck downloaded the Intersect 2.0. Luckily, Chuck's father may be able to help his son.
The Ring is closing in on Chuck and Operation Bartowski. Fortunately, Chuck's dad Steven is working hard to save his son. Meanwhile, Casey must secretly protect his daughter from the Ring, and Big Mike receives some serious news about the Buy More.
Shaw returns to threaten everything that Chuck holds dear as his friends, family and the woman he loves are all put in mortal danger. Chuck has to find Shaw and stop him before his own world gets torn apart.