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The episode opens with Chuck and Sarah never leaving their cabin on their train ride through Europe. In between sessions of consummating their new relationship, the two mutually agree to quit the spy business together. Independently, the two notice an obvious group of spies on the plane. Sarah through intuition and Chuck through flashing. They each go behind each others backs and manage to mutually discover a list of names of spies in the guy's cabin. They both come clean to each other and agree to go on one last mission together.
Meanwhile, Beckman sends Casey and Morgan to go and retrieve Chuck and Sarah who have gone AWOL. Morgan uses his creepy knowledge of Chuck to help them locate the guy and board the train. Casey arrives just as Chuck and Sarah are halfway through their plan of sedating the guy's guard and are about to capture the spy with handcuffs. Casey uses the handcuffs on Chuck and Sarah, who escape together and capture the spy. Soon the team learns that they just captured a spy who was being taken into witness proteciton by two Interpol agents.
The gang must now turn the spy into new Interpol agents they agree to meet at a cafe. Morgan's annoying questions reveal that new agents are actually evil and soon a fight breaks out where a handcuffed Sarah and Chuck save the day. They manage to hand the spy in and Chuck and Sarah come back home and eventually clean to each other they still want to be spies.
Back at home, Chuck meets up with Ellie just as she's grabbing her last object (cell phone) for her trip to Africa. Chuck managed to miss her tear-filled goodbye party, but she finally seems okay leaving her baby brother alone, knowing that he's "back" with Sarah.