Chuck's latest mission has him raiding a Malibu mansion to grab a million dollar diamond being used to fund terrorism. Tagging along is an attractive but less-than-trustworthy DEA agent.

Two new characters are introduced, both of whom want to take the Intersect. One is a beautiful, young female enemy agent that works in the Pita Palace next to the Buy More, and the other is a handsome CIA agent who is posing as an undercover police detective investigating a theft at the Buy More who wants to take Chuck into his custody. The former quickly blows Chuck's cover, while the latter kidnaps him and makes him vanish from his former life.

Chuck needs to go undercover to seduce a woman named Sasha Banachek, so an old school spy named Roan Montgomery is assigned as his mentor. Meanwhile, Captain Awesome finds himself in need of some relationship advice, and and turns to Morgan, and Lester faces his first problems as assistant manager.

Chuck, Sarah and Casey learn about a man called “Perseus” who is behind Fulcrum’s plans to build their own Intersect. While Sarah and Casey are sent to find Perseus, Chuck and Agent Cole Barker are forced to stay in a safety bunker. When the mission takes a dangerous turn, their orders to stay out of harm’s way go out the window. Meanwhile, Morgan tries to convince Anna that moving in with him would be a bad idea.

Chuck juggles his two lives as he trains new Nerd Herder Hannah and gets his very own asset who is caught up with The Ring. Chuck thinks he can handle his asset all on his own but Sarah and Casey feel the need to intercede. Meanwhile, Awesome must lie to Ellie when she starts to ask questions about Chuck and Morgan, Jeff and Lester do some recon work to learn more about Hannah.

After their first real fight, Chuck avoids confronting Sarah by going on a rogue mission that leads him to his mom's MI-6 handler, Gregory Tuttle, and a mysterious Russian agent. Meanwhile, Ellie is on her own mission to uncover the Bartowski family's long-buried past.

Chuck is put in charge of a top-priority mission, but his leadership skills are pushed to the limit when there is a murder in Castle. Meanwhile, Awesome takes on a mission of his own when Ellie finds an alarming new hobby. Elsewhere, Morgan's leadership is also tested when his Buy More troops wage war against Large Mart.

Chuck and Sarah track an assassin who is trying to eliminate the new intersect. Morgan tries to adjust to having the intersect. Jeff exposes a new side of himself.