Air date: 10/27/08

Life in espionage takes its toll on Chuck and everyone is taking notice. Chuck tries to explain his unusual behavior to Ellie and to the quirky Buy More efficiency expert Emmett Milbarge, but a new assignment only complicates things. After a global terrorist comes searching for Jeff, Chuck is forced to socialize with Jeff in order to find out what role the oddball plays in the mission. Sarah, Casey, and Chuck are all shocked when they discover that the fate of the world and the prevention of World War III rest in Jeff's hands and his ability to play the video game Missile Command, of which Jeff is the reigning World Champion. The designer of Missile Command is found to have also forayed into the command of actual missiles, and he had hid the launch codes to actual missiles within the video game. Chuck convinces Jeff to play an exhibition of Missile Command at the Buy More; however, when Jeff collapses under the pressure, Chuck is forced to play in his stead. Casey is ordered by General Beckman to launch an ICBM to destroy the satellite carrying the terrorist-controlled missiles, while Sarah drives to the TV station from which the terrorists are controlling the missiles. Chuck flashes and learns that Rush's song "Tom Sawyer" is the key to beating Missile Command. After finishing the game and recovering the launch codes, he phones Sarah with the information and the terrorist missiles are stopped. Chuck receives his degree from Stanford after Sarah and Casey use his field experience to supply the remaining needed credits.

Chuck vs. the Ex

Air date: 11/10/28

Chuck runs into his ex-girlfriend Jill Roberts while on a Nerd Herd call. In an attempt to save face, he lies to the girl who broke his heart and tells her that he is more successful than he really is. When Chuck flashes on Jill’s boss - a research scientist who may have developed a deadly bio-weapon, he, Sarah and Casey must find out if Jill is involved. Meanwhile at the Buy More, Big Mike nearly chokes to death, which leads company efficiency expert Emmett to implement a mandatory CPR course taught by Devon.

Chuck vs. the Fat Lady

Air date: 11/17/08

Chuck and Jill are enjoying the honeymoon stage of their rekindled relationship. However, Chuck's spy life intervenes when Casey and Sarah inform Chuck that he is needed for an immediate mission to recover a list of CIA Fulcrum agents that Guy LaFleur had apparently hidden in his hotel room before being murdered. Jealousy erupts when Jill finally meets Sarah and learns that Chuck and his handler must pose as a couple, especially when she learns that Sarah is posing as a seductively-dressed escort for the mission. Chuck does his best to reassure Jill that his relationship with Sarah is purely business but only finds himself in more trouble when Jill finds Chuck and Sarah in their hotel room in their underwear after trying to wash off a suspected bioweapon. The team recovers a music box in LaFleur's room, which leads them to the opera, where they recover an encrypted flash drive with the Fulcrum list. Chuck and Jill leave for a romantic getaway, during which Jill is kidnapped by Fulcrum and held hostage in exchange for the Fulcrum list. Chuck agrees to the exchange, but first makes a copy of the list with Morgan's Canadian copying device (designed to copy video games, but apparently able to copy anything). Chuck and Jill embark on another romantic getaway, during which Sarah and Casey discover from the recovered list that Jill is Fulcrum herself. Meanwhile, corporate efficiency expert Emmett is out to get Chuck and interrogates Morgan to get some dirt on his best friend. Morgan blackmails Emmett with footage of Emmett's drunken stupor.

Chuck vs. the Gravitron

Air date: 11/24/08

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. He willingly agrees to bring down the woman who betrayed him twice. Meanwhile, Devon's parents are coming for Thanksgiving and Ellie is determined to have the perfect Thanksgiving dinner. To make sure everything goes smoothly, she tells Morgan that he cannot come to dinner this year. Without any holiday plans to fall back on, Morgan is recruited by Big Mike to stand guard at the Buy More with Lester and Jeff.