On a train outside of Paris, Chuck and Sarah stay in their compartment, enjoying their getaway. A call from Beckman prompts them to agree to run away forever, afraid that spying will get in the way of their new relationship.
In Burbank, Ellie and Captain Awesome pack to go to Africa and Ellie wonders if Chuck will be back in time to say goodbye. Beckman orders Casey to find the couple, officially AWOL. She suggests he employ the use of Morgan, whose knowledge about Chuck might be useful.
On the train, Chuck and Sarah eat in the dining car, posing as the newlywed Charles's. Sarah spots two men with guns while Chuck flashes on a third man as the terrorist, Juan Diego Arnaldo. They do not point this out to each other, though Sarah smuggles a knife out in a napkin.
Casey and Awesome both approach Morgan at the Buy More to find out if he knows the whereabouts of Chuck. Morgan does not know, though he offers Casey his assistance. Jeff and Lester offer to Awesome to perform as Jeffster! at Ellie and Awesome's going-away party.
On the train, Chuck and Sarah go behind each others' backs to check out Arnaldo's compartment, and both nearly get caught in the process. Sarah eventually tells Chuck what she's seen and Chuck admits he also saw the terrorist. They agree to capture him.
In Burbank, Morgan and Casey use Morgan's knowledge of Chuck's eczema and addiction to Justice League to locate him on Paris security tapes. They fly to Europe.
Still posing as the Charles's, honeymooners from Texas, Chuck and Sarah distract Arnaldo and his men and slip narcotics into their drinks. Before they can capture him, Casey enters the train and handcuffs Chuck and Sarah. They escape and apprehend the terrorist. However, it turns out that he is in witness protection and his unconscious men are actually Interpol agents.
The team gets in touch with Beckman, who arranges another Interpol team to pick up Arnaldo. At a local cafe, Chuck and Morgan discuss quitting the spy life while Casey and Sarah do the same thing, all in front of Arnaldo. Casey tells Sarah to run before Interpol arrives. They leave.
Ellie and Awesome have their party in Burbank, but it is obvious Ellie is not happy without Chuck present.
Interpol agents come to the cafe to retrieve Arnaldo. However, they are soon revealed to be terrorists.
Chuck and Sarah leave back toward the train, but on the way there and while discussing the option of being spies and still being together, the Interpol agents they drugged capture them. The agents reveal the Casey and Morgan might be in danger.
Chuck and Sarah rescue Casey, Morgan, and Arnaldo. Arnaldo tells them that after hearing both their conversations in the cafe, neither of them really want to quit. Chuck and Sarah agree to return to Burbank.
In Burbank, Beckman congratulates them on their mission. Chuck and Sarah reveal their relationship and though she is not happy, she remarks that it's about time.
Chuck goes to Ellie's apartment and watches a video of her making a drunk speech about Chuck at the party. Ellie comes in to get her phone and they say goodbye.