Just as Chuck breaks into the CIA's mainframe to find Sarah, she walks in, bloody and claiming to have killed Quinn. A quick flashback shows otherwise. Chuck embraces his wife not knowing she's not really herself and that Quinn has tasked her to kill him.
But first Sarah has to find a pair of Intersect glasses for Quinn. She searches Chuck's belongings when he's not looking. Chuck notices all is not normal with Sarah when he witnesses her hack apart a chicken she's preparing for dinner and she shows little interest in getting romantic with him. Sarah finds the Intersect glasses while Chuck is asleep.
When he wakes up, he runs to Ellie for advice. He decides he needs to find the last Intersect program and destroy it. Sarah overhears his conversation with Ellie and then gets orders from Quinn to wait until Chuck finds the last program before she kills him. Sarah even tries to play along by getting affectionate with Chuck.
Shortly thereafter, Chuck enlists his team to break into the CIA's secret weapons lab and get that Intersect. Once inside, Sarah pretends to infect the Intersect with a virus, but actually she's downloading it onto the stolen glasses. She then grabs Morgan as cover and tries to make her escape, announcing that she's been working for Quinn and she thinks they are all evil. Chuck tries to appeal to their bond, and she seems drawn in by him, but then she pulls away, punches her husband in the face, and plants a bomb on her way out of the lab.
Quinn is waiting for her and detonates the bomb as soon as she hands over the glasses. But it turns out Chuck had seen that Sarah had stolen the glasses, so he replaced them with a fake pair, which means the glasses don't have the Intersect on them. Also, Chuck survived the explosion.
To get back at him, Sarah takes Ellie hostage and uses her as a bargaining chip for the glasses. The situation is grave enough that General Beckman calls in a CIA team to neutralize Sarah however necessary. They force Chuck to lure Sarah in to them.
Chuck tells Sarah where to meet him. As Sarah drives Ellie to the location, Ellie takes control of the car and deliberately crashes it, effectively knocking Sarah unconscious. Then, Chuck shows up and drives away with Sarah.
Sarah wakes up at home with her husband by her side. He does everything he can to remind her that their life together was special and important. She doesn't quite see it that way, and the two fight violently over the glasses, with Sarah slamming Chuck against a mirror and throwing him down the stairs of the house the dream house they built together.
Quinn shows up during the fight and even admits he was lying about Chuck's evilness. He gets the glasses from Sarah and then pulls a gun to shoot her. Chuck, wearing a bullet-proof vest, jumps in front of her to save her, but Quinn gets away with the glasses. Knowing that the CIA will be there soon, Sarah makes a run for it.
While Ellie and Devon console Chuck, Casey drops a DVD of Sarah's log entries chronicling the development of her feelings for Chuck over several years. It works, and Sarah realizes that Quinn had her fooled all along. She goes to Chuck to tell him she believes him, but she can't be with him, because the feelings are gone. She leaves, saying she needs to start her life over some how.