Chuck keeps Colt from getting the "Cipher," a device that would lead to a new Intersect. Chuck is told that this successful mission marks the end of his career and the beginning of a normal life. Chuck finally asks Sarah out on a date, but Chuck's role as the old Intersect is not good news for everyone, as Casey deals with a difficult order assigned to him. Meanwhile, Morgan comes up with an elaborate way of hiring a new assistant manager.
Chuck goes undercover to retrieve the Cipher from the Black Widow. In order to get close to his target, Chuck learns the art of seduction from Roan. Unfortunately, Roan is no longer the world's greatest spy. Meanwhile, Morgan gives Captain Awesome advice on his romantic night with Ellie, and Lester struggles to get respect as Buy More's new assistant manager.
Chuck is overcome with jealousy when his nemesis, Bryce Larkin, returns to the scene. Chuck and Sarah's latest mission requires Sarah and Bryce to pose as a couple, putting a strain on the relationship she has with Chuck. Meanwhile, Morgan must deal with a gang of bullies, from a neighboring sporting goods store called, the Mighty Jocks, led by Mitt.
Chuck learns more about Sarah's past. But when they run into her old high school nemesis Heather Chandler, Sarah's insecurities come to the surface and she tries to avoid Heather.
Chuck tries to explain his behavior to Ellie and to the Buy More efficiency expert Emmett Milbarge, but things are complicated by a new assignment. When a terrorist comes searching for Jeff, Chuck is forced to figure out what roll the oddball plays in the mission. Sarah, Casey and Chuck all get a big shock when they discover that the prevention of World War III rest in Jeff's hands.
Chuck lies to his ex-girlfriend about being more successful than he really is, after he runs into her will on a Nerd Herd call. When Chuck flashes on Jill's boss, a scientist who may have developed a bio-weapon, he, Sarah and Casey have to see if Jill is involved. Later at Buy More, Big Mike nearly chokes to death, which leads Emmett to enforce a mandatory CPR class taught by Captain Awesome.
Chuck and Jill are enjoying the honeymoon stage of their rekindled relationship. The two lovebirds plan a weekend getaway but have to cancel at the last minute when Casey and Sarah inform Chuck that he is needed for an immediate mission to find corrupt agents in the CIA.
Chuck, Sarah and Casey are shocked to discover that Chuck's girlfriend Jill is a Fulcrum agent in search of the Intersect. In the wake of his disbelief, Chuck is asked to use his relationship with Jill to get to an agent called Leader.