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Daniel Shaw is the main antagonist in season 3 of Chuck. He was a good guy and loyal member of team Chuck before he went rogue. Shaw was working with a terrorist team called the Ring and their main goal is to take over the CIA and NSA. So they will have federal agencies in their payroll. He also killed Chuck's father Stephen J Bartowski. Daniel Shaw is like the evil version of Chuck. That's the main reason why these guys are a lot alike. He eventually went to jail in the end of season 3.
He came back in season 5 to plan his revenge on Chuck. Clyde Decker was on Shaw's payroll on the CIA they never looked at; he ordered him to ruin Chuck and his friends' lives. Decker took the Intersect out of his head and all of them were fired from the CIA and NSA. Mostly he would throw the book at them for going rogue. Chuck has some strong evidence about his cover up turning Hartley Winterbottom (an MI6 agent) into a Russian terrorist named Alexei Volkoff that he can send to the press or the feds about his cover up. They let him go. Chuck and his team became freelance spies and figure out Decker was working for Shaw the whole time while he was in jail. Decker is dead and Shaw escaped from jail to have his revenge on Chuck and his team, but it backfired and he went back to jail.