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Even after realizing Sarah still has feelings for Bryce, Chuck must resume his cover of dating Sarah for a mission to stop a counterfeiter / yachtsman.
Bryce Larkin (Matthew Bomer) returns and he needs Chuck to help prove to Sarah and Casey that he's not a rogue agent.
Chuck starts to date Lou (Rachel Bilson), a sandwich-maker and things are going well until he discovers that she is part of a smuggling group.
Chuck struggles with his cover love life and his real one when he meets Lou (Rachel Bilson) who actually seems interested in him. Meanwhile, his cover relationship with Sarah heats up when they go on a double date with Ellie and Devon.
Chuck has to return to his Alma Mater, Stanford, on a homecoming weekend in order to help a former professor who Chuck finds out is a government operative being hunted for a top secret file.
Chuck runs into a runaway government agent that's in a similiar position to him, only his brain is valuable because he's a gadget whiz. Chuck must decide whether to turn this agent in or help him escape from his handlers.
When Chuck sabotages the mission of a Chinese spy, Mei-Ling Cho (Gwendoline Yeo), who was trying to save her kidnapped brother, Sarah and Casey refuse to help Chuck fix his mistake.
When a diamond hidden is Malibu is being used to fund terrorists, Chuck has to help steal it back. Sarah's friend Carina, a DEA Agent, shows up and tries to help in her own way.
Chuck gets a flash the lets him know an arms dealer known as "La Ciudad" will be at an art auction. Chuck infiltrates the party with Sarah and tries to identify the dealer.
A doctor is brought in to retrieve the data from Chuck's brain and he ends up murderered. Casey and Sarah turn against each other suspecting the other to be the killer.