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We meet up with Chuck during a spy training mission in Prague that he fails due to his emotion getting in the way of his Intersect flashes. Beckmen fires him and it sends Chuck into a downward spiral of not showering, being unemployed and on a cheesepuff bender. While out to get more cheesepuffs at the Buy More, he learns Sarah is still working on the yogurt shop. He goes to talk to Sarah, who is no longer answering his phone calls, only to get knocked out by Casey. He learns from Casey that he and Sarah are on a mission and sees the location on a laptop.
Chuck sneaks into the mission wearing his old Buy More outfit as a cover. We see Sarah on a date with a courier and after Chuck makes a scene, Casey and the other spies lock Chuck away so he can do no damage. While locked up, Chuck flashes when he hears a name, Javier, and knows there's an assassin there but can't get word out. When a member of the mariachi band walks he, Chuck flashes, knocks him out, and grabs his guitar to go out in his place. The mariachi member, Javier, turns out to be the the assassin and is about to shoot Sarah while she dances with her date. Chuck takes the couple down and Javier gets away. The several month mission is considered a failure and Casey convinces Sarah she needs to let Chuck down easy.
Meanwhile, Javier goes to the Buy More looking for Chuck and ends up shooting Emmett. The next morning at the Buy More, Sarah comes to talk to Chuck and the two end up getting kidnapped by Javier's men and brought to Mexico. Casey discovers Emmet's body on the cameras and rewinds back to find the cars in the parking lot to track him down.
In a flashback, we learn that Sarah asked Chuck to run away, but he chose to stay to become a spy.
Back in Mexico, Chuck flahses, beats up Javier, rescues Sarah and heads out. Chuck ziplines the two of them into more trouble and while in a standstill, Casey flies in a helicopter and shoots up the place, rescuing them. God it's good to have the team back.
Back at the Castle, Beckmen declares she's bringing back the team and their mission is the ring. For cover, Chuck and Casey get their jobs back at the Buy More. As a favor, Chuck gets them to get Morgan his job back, who was fired from Bennihana after Ana left with another cook. Back at home, Ellie and Awesome move out, and it looks like Morgan moves in at Chuck's roommate. In the courtyard, Sarah tells Chuck they can no longer discuss his feelings... he's a spy now. The episode ends with Casey and Chuck training.