Casey carries out a side mission for his old commanding officer James Keller that leads to him committing treason. When Chuck learns the dark truth about Col. Keller, he and Sarah set out to break Casey out of jail and clear his name. Meanwhile, Awesome's plan to keep Ellie out of danger gets more difficult when she gets her dream fellowship.

While in Europe, Sarah and Chuck realize they’re traveling on a train with Spanish spies. Even though they’re all alone, they decide to take on these rogue agents. Of course, this impromptu mission doesn’t go smoothly. Meanwhile, Beckman orders her newest “unlikely” spy team – John Casey and Morgan Grimes – to track down the missing couple.

After his last dream, Chuck asks Morgan to help him on a side mission. Their investigation becomes complicated when Stephen J. Bartowski returns and learns that Chuck downloaded the Intersect 2.0. Luckily, Chuck's father may be able to help his son.

When Chuck go undercover in Milan, Chuck realizes the "Achilles' Heel" in their relationship, but must set personal issues aside for the mission. Meanwhile, Morgan recognizes a fatal flaw that compromises the new Buy More. Elsewhere, Casey struggles to put down roots in Burbank.

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.

The mission to take down Volkoff reaches a dangerous new level, while big changes loom at home. As Sarah works to free Chuck’s mom, Chuck and Morgan embark on their own mission to take down Alexei Volkoff. Meanwhile, Casey bonds with his daughter, Alex, while Ellie tries to ease Awesome’s anxieties over fatherhood.

Valentine's Day is interrupted when Chuck and the team are sent on a mission to England to protect a reclusive young heiress, Vivian McArthur. Meanwhile, Casey gets an offer from the mysterious Jane Bentley. Back at home, Ellie and Awesome find an unlikely solution to a parenting problem, as Morgan ponders a big move.

When Chuck and Sarah get conned out of their wedding money, there is only one man they can turn to for help -- Sarah's conman father, Jack Burton. Meanwhile, Morgan pressures Casey to face Alex's mother.

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.

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.