It's the end of the road for Chuck. And there's a lot at the end of that road: laughter, tears, and romance, even if it's not in the way you might want.
Sarah, still believing the villainous Quinn (Angus MacFadyen) is her handler, is making Chuck more than a little confused. Faced with the idea that he almost lost her and Morgan because of the Intersect, he launches a mission to destroythe thing that changed his entire life. He's shocked when Sarah uploads the Intersect instead and leaves the whole team trapped in the lab. Even she is surprised when Quinn activates the explosive he had her place, ostensibly blowing Team Bartowski to kingdom come.
While the team staggers free, Sarah meets Quinn and slugs him, but hands him the Intersect glasses. They say "no data," however, and she realizes that Chuck must have switched the glasses out in their confrontation. She decides to take Ellie hostage in exchange for the Intersect. This attracts the attention of General Beckman, who tells Chuck to get Sarah to a nearby plaza where she's bringing backup, including Casey with a sniper rifle. "She's not in there anymore," Casey tells Chuck. "Sarah's gone." But Chuck refuses to give up on his wife and goes off-book. Meanwhile, Ellie takes matters into her own hands, forcibly crashing her car to knock out a seat belt-less Sarah.
Over Ellie's objections, Chuck takes an unconscious Sarah to their dream house and tries again to convince her that he was more than just an assignment to her. We get some handy flashbacks (wow, look at Zachary Levi's early-season hair!) and some heartwrenching crying. Anyone who's ever doubted Levi's acting skills should watch this scene and be convinced that he can act. Unfortunately, it doesn't go too well. She's unconvinced, and he refuses to fight back as she beats the living daylights out of him before taking the Intersect glasses back.
What finally turns her head is seeing where she carved their names into one of the beams in the living room. But Quinn shows up a minute later, admitting that he used Sarah and trying to shoot her. Chuck takes the bullet for her instead, urging Sarah to flee before Casey and the CIA team can capture her. Casey, however, tracks Sarah to her apartment in order to give her a copy of her own mission logs on DVD, so that she can see for herself who she used to be.
She shows up at Chuck's apartment to tell him that she believes everything he said, but she doesn't feel it. "Most of all, I wanted to say goodbye," she tells him. "Quinn took away my life, and well, I have to go find it." He reluctantly lets her walk away.
Two weeks later, Quinn is picking up one piece of an Intersect key on a private jet, but Sarah is hiding amongst the baggage. The two of them get into an armed standoff, but unable to put him down thanks to some engineered turbulence, Sarah blows open the plane's door and does some awesome skydiving.
Meanwhile, her husband is being a sad bastard, surrounded by his family (and Morgan). "I can't get her to fall in love with me again," he moans, but Ellie is optimistic. "She fell in love with you before, Chuck," she reminds him, and this gets Chuck out of bed with a new mission - even if it means he has to "unleash the perverts," in the words of Jeff and Lester. He's shocked when she arrives at the Buy More, asking for access to Castle and his help finding the arms dealer Quinn is meeting. She plans to show up, kill Quinn and disappear forever.
Chuck convinces Sarah to let him and Morgan accompany her to Berlin. Casey is also headed there, having gotten the order from Beckman to make Quinn "very dead." Trying to keep tabs on the arms dealer leads them through locations reminiscent of their early years, such as a Mexican restaurant and a Weinerlicious. However, Quinn shows up, shoots the arms dealer, and Chuck accidentally shoots down Casey's helicopter with a poorly aimed warning shot. Whoops.
Mission failed, Chuck has Sarah upset with him and Casey tells Morgan that he's leaving. Morgan calls Casey a "giant jackass" and convinces him to spring Chuck and Sarah to help him find Quinn. Mama Bartowski shows up to reassemble the entire team, including Ellie and Awesome, and brief them about the Intersect key. It gives Ellie the idea to swipe the Intersect glasses and try to use them to restore Sarah's memory, by not uploading the Intersect, but a specific file for Sarah including things like her dossier and wedding album. Unfortunately for everyone, Quinn is one step ahead of them, having gotten the drop on General Beckman and the final piece of the key.