Without the Intersect in his head or the support of the CIA, the world of espionage is a much more dangerous place for Chuck Bartowski and his team of freelance spies. To start, Carmichael Industries takes on a slick, rich thief named Jean Claude, and a conniving investor, Roger Bale, who has stolen money from some of the world's most dangerous people. Meanwhile, Morgan helps Chuck with a special surprise for Sarah. Back in the Buy More, Jeff and Lester have taken things to another level with their latest scheme.

As the team takes on a missing persons case, Chuck and company struggle to establish themselves as Carmichael Industries in the face of a rival security firm led by the tough and efficient Gertrude Verbanski. Meanwhile, Morgan continues to adjust to the Intersect while Chuck adjusts to being his handler. Also, the Buy More finds an unlikely spokesperson to help drum up business.

As the team is tasked with finding one of the CIAs most wanted, Chuck fears that the Intersect may be going to Morgan's head. Meanwhile Sarah helps Casey navigate his relationship with Gertrude. Elsewhere, Captain Awesome makes a startling revelation about Jeff and Lester.

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.

Chuck turns to Verbanski for help tracking a computer virus. Lester and Jeff's relationship is complicated by a new Buy More employee.

Chuck and Sarah must race against time and a ruthless spy Robyn Cunnings, to destroy a dangerous computer virus. Meanwhile, Ellie and Awesome are spending their date night which takes on a dangerous turn and Morgan is sent on a special mission to recover Chuck's P.A.N.T.S.

Sarah is forced to confront a secret from her past and feels she must do so alone, while Chuck urges her to let him help. When Sarah encounters her original handler, Kieran Ryker, she fears that he will harm those closest to her, including her mom.

While Chuck and Sarah contemplate the next step for Carmichael Industries, Casey’s forbidden love, Gertrude Verbanski, walks back into his life with a questionable mission in South Beach. Meanwhile, Jeff’s enhanced intelligence leads he and Lester to suspect that something unusual may be happening at the Buy More.

As Chuck and Sarah try to realize a new, safer future, Morgan’s past as the Intersect sends them to Vail on one last mission, where they enlist the help of an unlikely source — the legendary Bo Derek. Elsewhere, Jeff and Lester continue their own spy mission.

When a mission in Japan becomes a hostage situation, Sarah and Chuck must face the merciless Nicholas Quinn aboard a speeding Japanese bullet train. Meanwhile, the mission leaves Casey with an impossible decision.

After a harrowing mission, Sarah returns to Chuck with a huge secret. Meanwhile, Ellie and Awesome are presented with a new opportunity that could change their lives.

Chuck enlists his family, friend and some unexpected allies as he races to stop Nicholas Quinn from destroying everything Chuck has built over the past five years.