Chuck springs into action to protect a visiting dictator (Armand Assante) who's targeted for assassination, yet Chuck must capitalize on his friendship with Awesome to get the job done. Awesome delights in the exciting spy jinks, but Chuck fears he's putting Awesome and Ellie in danger.
When evil operative Sydney Prince (Angie Harmon) mistakes Awesome for being a master spy, Chuck responds by serving as Awesome's handler and tutoring him in the fine art of spying. While on a mission, they encounter an enigmatic man (Brandon Routh). Meanwhile, a promoted Morgan becomes assistant manager, but that means he has to deal with Jeff and Lester's tomfoolery.
It's a French connection for Chuck when he departs to Paris for his first solo assignment. During the flight, he connects with a woman (Kristin Kreuk), but the trip turns turbulent when he tangles with a menacing passenger ("Stone Cold" Steve Austin). Meanwhile, Morgan battles Jeff and Lester for power at Buy More. Brandon Routh also guest stars.
Continuing his taxing quest to balance his two lives, Chuck must train new Buy More employee Hannah (Kristin Kreuk) while his spy work involves handling his very own asset, a scientist who's entangled in a nefarious organization. Meanwhile, poor prevaricator Awesome must lie to Ellie about Chuck's undercover endeavors; and Morgan, Jeff and Lester snoop into Hannah's background.
In a surprise spy maneuver, Agent Shaw (Brandon Routh) pairs Chuck with Hannah (Kristin Kreuk) for a mission. Shaw thus teams up with Sarah---but it might be his ploy to inch closer to her. Meanwhile, Morgan and Ellie snoop into Chuck's secret world.
Chuck promises to prepare dinner for Hannah (Kristin Kreuk), Ellie and Awesome. But it's a pressure cooker before all that: Chuck goes on a mission and must pose as the world's most lethal assassin. Elsewhere, Sarah resolves to keep her relationship with Shaw (Brandon Routh) purely professional.
Chuck loses his ability to "flash" and is forbidden to participate in a mission. But with his spy peers out on assignment, troublesome forces affect the benched Chuck back at the base. Brandon Routh recurs as agent Daniel Shaw.
When Casey sets out on a side mission for his former commander (Robert Patrick), he lands in jail for treason. Cut to Chuck and Sarah, who try to break him out of prison and restore his good name. Meanwhile, Ellie scores a coveted fellowship, which makes Awesome's efforts to protect her all the more difficult.
Chuck's future in the espionage business rests squarely on a final test mission that will determine his worth as a spy. With Sarah and Shaw (Brandon Routh) appraising his every maneuver, Chuck must tap into all he has learned in order to make the operation a success.
When Chuck is able to take his pick of the finest CIA agents for an undercover mission, he considers only one very special superspy---Sarah. Enter Casey, Morgan and Awesome, who try to help him win her back.
The spies regroup upon discovering that a villainous operative was responsible for the death of Shaw's wife. They spring into action to find the evildoer---but Chuck worries about Shaw's psychological state. Meanwhile, Morgan mulls over leaving Buy More. Brandon Routh recurs as Shaw.
An adventure awaits Chuck and Sarah in Europe when they encounter Spanish spies on a train. Although lacking any backup, it's full steam ahead for the couple when they try to derail the spies' agenda. And an odd-couple spy team emerges: Casey and Morgan, who set out to help Chuck and Sarah.
Chuck and Sarah train under the tutelage of a married CIA team (Fred Willard and Swoosie Kurtz), who have a glowing record together but despise one another. In another training mission, Casey must show the spy ropes to an unlikely student---Morgan.
When Chuck experiences alarming nightmares, Gen. Beckman forces him to see CIA psychologist Leo Dreyfus (Christopher Lloyd). Meanwhile, Ellie receives big news; and Anna (Julia Ling) returns to the Buy More and reaches out to Morgan.
Chuck enlists Morgan's help for a side mission, but the assignment turns complicated upon the arrival of Chuck's father (Scott Bakula), who discovers that an advanced version of the Intersect has been downloaded into his son.
Shadowy thugs from the Ring inch closer to take down Chuck and his team. Elsewhere, Casey undertakes a clandestine mission to protect his daughter from the Ring; and big news about the Buy More floors Big Mike.