Returning to Stanford, the University that expelled him, Chuck has to help a former professor who is a government agent being hunted for a sensitive top-secret file he has in his possession. At the same time, Chuck learns much about himself and about the death of his friend Bryce Larkin.

Chuck goes undercover at Sarah's 10-year High School reunion, where they meet the girl that tortured Sarah back in the old days.

Chuck gets jealous when Sarah has to seduce a Fulcrum agent. Meanwhile, Jeff and Lester start looking for the "Buy More Babe" as a way of finding a new employee.

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.

Casey, Chuck and Sarah are sent to Morocco to rescue Roan Montgomery. Morgan plans to meet Alex's mother and Mary spends some time with her family.

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.

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.