Clyde Decker was described as the CIA's toughest and best agent. He was sent to stop Chuck Bartowski from committing treason by requesting aid from Hartley Winterbottom to save Sarah, first appearing in the Season Four finale episode "Chuck Versus the Cliffhanger". His capabilities and reputation can be ascertained from the fact that he frightens John Casey.
Decker speaks directly to Chuck when the latter tried to break Volkoff out of prison to counteract the Norseman. However, Decker already transferred Volkoff elsewhere before the arrival and fires Chuck from the CIA. Decker then issues an arrest for treason to cover up any conspiracies with regard to Agent X.
Later, Decker removes the faulty prototype Intersect from Volkoff before Chuck could hijack the transfer truck, returning Volkoff's original identity as Hartley Winterbottom and ultimately Agent X. Nonetheless, Hartley follows Chuck after recognizing him as the son of Stephen Bartowski and creates a temporary cure for the Norseman.
Decker eventually captures Chuck, Mary, Casey and Hartley outside Westside Medical and debriefs them at Castle. There, Decker removes the Intersect 2.0 from Chuck and attempts to convince Casey to tell the Bartowskis that the Intersect project is over. Casey figures out that Decker wants them to make a run for it so that he can look like the hero. He then got the jump on Decker and helped his friends escape.
Later, Decker and a team of CIA agents were waiting outside Westside in anticipation of Chuck's return after he acquired the antidote from Vivian Volkoff. Decker felt that he had beaten Chuck when his agents outnumbered Team Bartowski and the CAT Squad. However, Chuck brings in Russian Spetsnaz units from Volkoff Industries and forces Decker to stand down. Chuck then threatened to leak the truth about Agent X and Decker's involvement if he dared to harm his friends and family.
Decker still has the entire Team Bartowski fired, however, Chuck states that he's done with the CIA.
At the end of the season four finale, Decker revealed that everything that has happened to Team Bartowski had been part of the plan, and that Chuck was merely a pawn. The plan has many parts like Fulcrum, The Ring, Daniel Shaw, Agent X, The Omen virus and more. The main objectives of the plan is to eliminate Chuck Bartowski and his team.
In "Chuck Versus the Zoom", Decker foils Carmichael Industries as they attempted a heist on Roger Bale by freezing all the money they were attempting to steal, including the Volkoff assets - leaving them with nothing but the Buy More and Castle, and sounds the security alarm.
Decker is a key member of a group of rogue CIA agents, determined to see Chuck fail. However, at the end of "Chuck Versus the HackOff", Decker is killed by Gertrude Verbanski with the use of an explosive, which she switches for the computer virus he believes he is obtaining. In "Chuck vs. the Santa Suit", it was revealed that Decker was indeed corrupt beforehand and was blackmailed by prisoner Daniel Shaw when the latter discovered it. Through this, Shaw was able to manipulate Decker into hunting down Chuck and ultimately removing his Intersect 2.0.
Decker blackmails and coerces Chuck and the team into stealing a terrifying computer virus when he threatens the life of the imprisoned John Casey, but this is his last slip-up, as Gertrude Verbanski takes steps, and a small explosive, to ensure Decker won't be complicating anyone's life again.
While disavowing all knowledge of his illegal activities and persecution of Team Bartowski, the CIA is offended by his 'removal' from the game, and his masters continue to send further pawns against the heroes.