Air date: 9/29/08

Chuck prevents Col from obtaining the Cipher – a device that would ultimately lead to a new Intersect. Chuck is told that this successful mission marks the end of his espionage career and the beginning of a normal life. Free from bullets and bombs, Chuck finally asks Sarah out on a real first 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 – that Chuck must be terminated when the new intersect is activated. Meanwhile, at Buy More, Morgan develops an eccentric way to hire a new assistant manager. In the end of the episode, the Cipher is revealed to be implanted with a virus by Fulcrum, and exploded when activated.

Chuck vs. the Seduction

Air date: 10/6/08

Chuck must go undercover to retrieve the Cipher from Sasha Banachek, known as the Black Widow. But in order to get close to his target, Chuck must learn the art of seduction from the legendary debonair spy Roan Montgomery. Unfortunately for Chuck, Sarah, and Casey, Roan is no longer the world's greatest spy. Meanwhile, Morgan offers Devon some advice for a romantic night with Ellie, and Lester struggles to gain respect at Buy More as the new assistant manager.

Chuck vs. the Break-Up

Air date: 10/13/08

Chuck is overcome with jealousy when his nemesis Bryce Larkin, Sarah’s ex-lover and partner, makes an unexpected return. Chuck and Sarah’s growing feelings for each other are tested when their latest mission requires Sarah and Bryce to pose as an extremely affectionate couple. Meanwhile, Morgan faces his own challenge at Buy More when he must deal with a gang of bullies, the Mighty Jocks. Led by Mitt, these bullies are the employees of a neighboring sporting goods store, and they love to take over Buy More's home theater room to play sports video games.

Chuck vs. the Cougars

Air date: 10/20/08

Chuck learns more about Sarah’s past when they run into her old high school nemesis Heather Chandler. Sarah’s teenage insecurities come to surface and she tries to avoid Heather at all costs. Chuck, on the other hand, does everything he can to hear more about Sarah’s hidden life. When Heather’s nerdy husband Mark turns out to be a key player in a new mission, the agents must attend Sarah’s high school reunion to prevent the sale of potentially dangerous super-bomber plans – all the action ends with the ultimate cat fight. Meanwhile, Big Mike leaves town for a day and Buy More’s new assistant manager Lester decides to implement a new sales policy.