Chuck retrieves the Cipher—the final piece needed for the new Intersect—from a formidable operative named Colt. With the new Intersect almost up and running, Chuck asks Sarah on a real date and begins to think about moving forward with his life and away from the Buy More. Meanwhile, Casey receives an assignment that will not be easy to fulfill.

The "Cipher" is stolen by Sasha Banacek and the team calls in legendary spy Roan Montgomery to give Chuck lessons in seduction. Chuck gets close enough to Sasha to steal back the Cipher, but Sasha kidnaps Casey and Sarah and uses them as hostages. Now only Roan can help Chuck save the day... and Roan isn't the spy he once was.

Chuck finds himself working with Casey, Sarah and Bryce and they're after a decrypted microchip which a Mr. Von Hayes has. Chuck again gets jealous when Bryce and Sarah go undercover together at a lavish party thrown by Mr. Von Hayes and he nearly blows his cover as a waiter. Chuck does manage to make a deal with Von Hayes for the microchip. Lester is now in upper management at Buy More and wants to use his position to delegate a task for Morgan to get the jocks out of the home theater room.

At her new job at the Orange Orange, an old friend of Sarah shows up and reveals her real name as Chuck was listening in and decides to have some fun with it to the point of almost giving away her cover. He decides to obtain more info about Sarah when the girl's husband shows up and Chuck has a flash on him. Chuck, Casey and Sarah go undercover at Sarah's high school reunion and stop the sale of high-tech bomb plans getting into the hands of Russians.

A terrorist comes looking for Jeff, and Chuck is forced to bond with his co-worker to find out why he's in demand. Meanwhile, Ellie wonders about Chuck's ambitions, and a new efficiency expert, Emmett Milbarge, arrives at the Buy More to see who is slacking off and bringing down the store.

Chuck bumps into his old flame Jill from Stanford while out on a Nerd Herd call. While they reacquaint themselves, Chuck lies by saying how successful he has been. But a flash on her boss has Chuck seeing a scientist who developed a bio-weapon. So it's up to Chuck, Sarah and Casey to find out if she's involved. Back at Buy More, Big Mike almost chokes to death. Emmett, the company efficiency expert, makes it mandatory that all employees learn how to perform CPR from Captain Awesome.

Chuck, Sarah and Casey are investigating the CIA for corrupt agents. Things between Chuck and Sarah become complicated when he reunites with his old girlfriend from Stanford. Even having Sarah and Jill meet doesn't help Chuck out despite his explanation that he and Sarah merely work together. Meanwhile, Emmett the company efficiency expert at Buy More is out to get Chuck through his best friend, Morgan.

Chuck, Sarah and Casey are surprised to learn that Jill, Chuck's girlfriend, is a Fulcrum agent searching for the Intersect. Because of this, Chuck is asked to use his relationship to get to an agent named "Leader." Meanwhile, Captain Awesome's parents are coming for Thanksgiving and Ellie is determined to make the perfect dinner for them.

Chuck is put on a mission in hopes of getting him to forget about Jill. Meanwhile, Casey learns his sensei mentor is one of the most wanted agents, leading him to be removed from the case. Elsewhere, as their wedding day nears, Ellie and Awesome receive a visit from Awesome's parents, and Emmett holds an Employee of the Month contest.

Chuck decides to spy on Sarah and her date and as he does so, Chuck has an Intersect flash about him. Meanwhile, Anna asks Morgan to move in with her.

On Christmas Eve, a burglar puts a damper on everyone's plans. Chuck, Ellie, Awesome and the Buy More employees are taken hostage and Casey and Sarah must go to any lengths possible to protect Chuck.

When an assassin tries to kill rock star Tyler Martin, Casey and Sarah take him into protective custody and try to figure out his connection to African agents. Meanwhile, Big Mike asks Morgan to take care of his parolee friend Butterman, and Chuck's knowledge of Sarah's killing of a FULCRUM agent begins to take its toll on him.

It is Valentine's day and emotions are boiling at the Buy More. However, Big Mike has to face a divorce, so the Buy More team try to distract him. Meanwhile, Chuck and Sarah go undercover as a married couple in the suburbs.

When Anna's new boyfriend turns out to be connected to the Triads, Chuck is ordered to spy on him by becoming his friend, thereby endangering his friendship with Morgan. Meanwhile Jeff and Lester want to perform at Ellie and Devon's wedding with their band called "Jeffster!"

Sarah has to seduce a Fulcrum agent, and Chuck isn't too thrilled. Meanwhile, Morgan moves in with Chuck while Big Mike dates his mother, and Lester and Jeff recruit the new "Buy More Babe."

Sarah and Casey lock Chuck up with MI 6 agent Cole Barker and go hunting for the Fulcrum scientist behind the plan to recreate the Intersect. Meanwhile, Morgan tries to get out of moving in with Anna so he can move in with Chuck, unaware that Chuck is moving in with Sarah.

Chuck finds out the name of the mastermind who developed the Intersect which is embedded inside his head. He must decide who he can trust---Sarah and Casey, or the mysterious scientist who could erase the Intersect from his mind. Meanwhile, a conflict arises between the Burbank and Beverly Hills branches of Buy More.

A cold female agent is sent in to evaluate Sarah's performance, now that their complex relationship has been unveiled, which may cost Sarah her job. Meanwhile, Morgan and "Jeffster" (Jeff and Lester) hope to get an invite to Awesome's bachelor party.

Chuck feels his life is finally coming together when his absent-father returns and Chuck gets to work with computer magnate Ted Roark in his dream job. But neither wind up being much of a dream.

Fulcrum has kidnapped Chuck's father and Chuck discovers that to find him he must get help from his ex-girlfriend, Jill Roberts, the person he mistrusts the most. Meanwhile, the Buy More team tries to sabotage Emmett's corporate evaluation.

Chuck and Casey flee to find Chuck's dad, disobeying Beckman's orders. However, Casey soon tracks them down and has to make a major decision. Meanwhile, Morgan is forced to become Emmett's assistant manager but things don't turn out as planned, and Devon makes a major discovery.

It's Ellie's big day. Chuck must save her life and her wedding from being ruined by Ted Roark and Fulcrum.