Chuck, holding the Cipher in his hand, is interrogated as he was being held off the side of a building by a large man named Colt (as will be revealed later). Hesitant to reveal the true story about him accidentally downloading government secrets into his brain, Chuck just blabbers on that he was a very important government asset working part-time for the NSA and the CIA. As he was about to be dropped by Colt, Casey and Sarah enter the room and save him.
Back at Casey's place, General Beckman and CIA Director Graham reveal that the new Intersect is about to come online after the retrieval of the Cipher, and that Chuck's life as a spy will soon come to an end. Chuck walks out of the apartment with Sarah. Even as he is relieved that he will get his old life back, Sarah tells him that he can do anything he wants with his life. Meanwhile, Casey is instructed by General Beckman to eliminate Chuck.
Chuck wakes up at 7:00 AM the next morning and prepares for work. Stepping into the bathroom, he is shocked to see his sister Ellie showering with her fiancé Devon. During breakfast, Chuck discusses his new-found desire to redirect his life and career. As he enters the Buy More, Morgan meets with him and lays out a blueprint and a plan on how to finish the game Call of Duty. Chuck then thanks Casey for everything he's done for him.
Big Mike offers Chuck the position of Assistant Manager of the Buy More. He turns down the job so he needs to interview the employees to fill the position. Chuck goes to Orange Orange, the new shop Sarah is working at. He invites her out on a real dinner date, and Sarah accepts the invitation.
Later that evening, Chuck and Sarah dress up for their first date, as Casey prepares to assassinate Chuck. Before his date, Morgan picks him up at his place to go through their Call of Duty game plan again. Meanwhile, at Casey's apartment, an impostor tricks Casey into giving him the cipher and sprays Casey with a lethal gas.
At the Chinese restaurant, Chuck tells Sarah how smart, cool and beautiful she is. Back at the apartment, Casey barely escapes death by turning on the ceiling sprinklers and injecting himself through the heart. Just as Chuck and Sarah were about to kiss, Chuck flashes on several individuals in the restaurant, and Colt enters with several armed men. But then, Casey drives through the restaurant to save them both. Colt punches Casey in the face before they drive off.
The next morning, Chuck goes to his regular job at the Buy More and contemplates his fate and future. With help from Morgan, Chuck interviews Anna, Lester and Jeff for the position of Buy More Assistant Manager. Casey then enters the room to place a band-aid over the wound in his face. As Chuck sees the mark left by Colt's ring on Casey's cheek, he flashes with the location image of Colt's hideout.
Sarah and Casey prepare to raid Colt's hideout, as Chuck is left behind at the Buy More. Meanwhile, Morgan organizes the "Thunderdome", a cage match tournament to determine who the new Assistant Manager will be. Big Mike sends Chuck out to respond to a computer emergency call, which turns out to be a trap set up by Colt, while Casey and Sarah finds nothing at the location Chuck gave them.
Before Colt terminates Chuck, Chuck bluffs him into thinking that the building is surrounded by "23 infantry troopers, 16 snipers, seven heavy-gunners, four demolitions experts and enough ammunition to orbit Arnold Schwarzenegger". It is the same specs he and Morgan have for their Call of Duty game plan. While Colt looks out the window, Chuck runs away with the Cipher. Colt catches up with him, and Chuck again finds himself hanging off the side of a building. Colt drops Chuck, but Casey, who is coming up the fire escape, catches him by the arm. Sarah gets into a fight with Colt. Casey reaches the roof and holds a gun at Colt, but then Colt's armed goons step onto the roof. Chuck enters with his own team and arrests Colt and his men.
Back at Casey's apartment, General Beckman and Director Graham reiterate the need to eliminate Chuck. Casey tries in vain to convince the General to spare Chuck's life. At Chuck and Ellie's place, Chuck prepares dinner for him and Sarah. Ellie and Devon leave for their dinner date.
While the new Intersect is being prepared to come online, Casey enters Chuck's apartment through the window. CIA Director Graham proceeds with initializing the new Intersect, as Chuck, unaware of Casey sneaking in on him, continues to set the dinner table. With a message of thanks from Fulcrum, the new Intersect computer goes off, and the room filled with video walls explodes, with Director Graham and several government agents in it. As Casey is about to shoot Chuck, Sarah rings the doorbell and tells Chuck about the unfortunate incident with the new Intersect.
The next day, Chuck sits on his Nerd Herd desk and talks to Morgan about his future. Morgan then invites him to watch Jeff consume 90 Twinkies in three minutes. Chuck, Casey and Morgan leave their posts to do just that.