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Chuck finally finds out that Jill is a Fulcrum spy but he's forced to go on dating her in order to try and capture her boss, code named Leader.
Things are going well with Chuck and his rekindled relationship with Jill, until Operation Bartowski must acquire a list of FULCRUM agents left behind by Guy Lafleur.
Chuck runs into his ex-girlfriend (Jordana Brewster) while on a Nerd Herd call. In an attempt to look cool to her, he lies and claims he's more successful than he is.
When a global terrorists comes looking for Jeff, Chuck finds out it's about Jeff's ability to play Missile Command and that real world launch codes are hidden within the game.
Sarah runs into her old high school nemesis Heather Chandler (Nicole Richie) and Chuck learns about her past, teenage life.
Bryce Larkin returns and Chuck becomes jealous when Bryce and Sarah are sent on a mission as an affection couple. Meanwhile, Morgan must deal with bullies at the Buy More.
Chuck must go undercover to retrieve the Cipher from Sasha Banicek (Melinda Clarke), aka The Black Widow. In order to seduce her, Chuck must train with Roan Montgomery (John Larroquette).
Chuck prevents Colt (Michael Clarke Duncan) from obtaining a device that would lead to a new Intersect. Chuck is told this was his final spy mission.
Captain Awesome asks Chuck if he can have Ellie's hand in marriage and when Chuck agrees he makes Chuck hold on to the ring for him.
Chuck discovers that Russian arms dealers at meeting in Los Angeles and one of the Russian women, Ilsa Trinchina (Ivana Milicevic) flashes for him as Casey's ex.