Sarah keeps an important secret from Chuck in order to ensure the success of a mission. Ellie and Awesome receive some life-changing news.
- Chuck (Zachary Levi) is scared to death about Sarah. He knows Nicholas Quinn () wants the Intersect and will use Sarah to get it. He hacked into a CIA database to find a DARPA (Defense Advanced Research Projects Agency) warehouse he thinks contains the final Intersect. Casey (Adam Baldwin) and Morgan (Joshua Gomez) are ready to go and head out the door...to find a bloodied Sarah (Yvonne Strahovski) limping in. She tells the story of what happened. Quinn tried to convince her she had been undercover for the past five years observing a rogue spy named Chuck Bartowski. And Quinn wants her to kill him. Only she doesn't, and takes him out, throwing him out the window of her hotel. She tells Chuck, Morgan, Casey, Ellie (Sarah Lancaster), and Devon (Ryan McPartlin) that Quinn is dead...exactly the way Quinn wanted her to. Quinn talks to her on a barely-there earpiece, giving her instructions on how to proceed. It turns out she threw Quinn out the hotel window and hung on (still not sure how a 110-pound person holds on to a 250-pound man dangling out a window, but whatevs). Quinn shows her the video recording she made right before she met Chuck. Quinn also tells her Chuck is responsible for the deaths of Langston Graham and Bryce Larkin.
Even with Sarah being back, Chuck was still apprehensive about what the Intersect had done to his family, and Sarah was acting a bit "off". A fact he discusses with Ellie just as Sarah was about to retrieve the Intersect glasses and kill Chuck in his sleep. Ellie, who received a job offer to a medical center in Chicago along with Devon ("Babe, we're being wooed . . . by Midwesterners!"), told Chuck to be patient with Sarah, even though some of the little things weren't happening, such as Sarah warming up her cold feet in bed by using Chuck's. Sarah overhears all of this, as does Quinn. Chuck is convinced he has to destroy the Intersect, so Quinn tells her she has to go with and download the Intersect onto the glasses before killing him. She agrees, and even remembers to cuddle up to Chuck (especially his feet) when he gets back.
Chuck meets with the rest of Team Carmichael, who agree the Intersect has done more harm than good. They head out. Chuck finds the Intersect glasses in Sarah's bag, which made him instantly suspicious. At DARPA headquarters, where it really did look like where Q from the James Bond films would play, the employees are hit with knockout gas, and the team enters through a vent. (Morgan loved the cloak of invisibility they were working on...perhaps too much for everyone's liking.) They find the Intersect room, only it has five guards. Sarah pulls a little Bryce Larkin from the pilot episode and uses some ass-kicking gymnastics to take them out. They find the familiar room. Chuck uploads the virus to destroy the Intersect. While he's doing that, Sarah takes out the glasses and downloads the data. She then takes Morgan hostage and tells Casey to drop his gun. She tells them about what Quinn told her. They try to convince her the Intersect she has is damaged. She lets Chuck get close, knocks him out and escapes from the Intersect room, locking them inside and setting it to explode. Except Sarah didn't want to blow them up, since they'd be arrested. Quinn overrules her and detonates the Intersect room.
Of course, since this is a two-hour finale, everybody survives. And even better, Chuck switched the glasses when he tried to convince Sarah to not listen. Sarah wasn't happy with Quinn, but Quinn was less happy when he found the glasses to be empty. Lucky for Sarah, Chuck called, so Sarah promised not to make the same mistake twice. Chuck, naturally, was panicking. Morgan was panicking even more. ("Dude, she's totally evil! OK, that was a bit unfair, but that was the bad Intersect talking. It's like me with my faulty Intersect, only much, much worse!") Casey was calmer but much more dire. He thinks Sarah is gone and would even go so far as harming Ellie and Awesome to get the glasses. Chuck is beside himself but calls Awesome. Unfortunately, Ellie went to get a cup of coffee with Sarah, obviously not knowing what's going on. Chuck tries to call Ellie's phone, but Sarah gets it first. She tells Chuck to bring the glasses to her in fifteen minutes. General Beckman (Bonita Friedericy) was read in on what was going on, told Chuck to go to the meet but tell Sarah he hid the glasses in Regal Plaza. Chuck doesn't want snipers to take Sarah out. Beckman said Ellie and the glasses were the priority. What happened at the plaza would depend on Sarah. Chuck goes to the cafe and promises to take Sarah to the glasses, only Ellie will drive Sarah to the pickup.
They drive over. While Chuck tells Casey, who was waiting with his sniper rifle, that Sarah has Ellie, Ellie tells Sarah she didn't have to do this. Sarah was there for her wedding and to see her baby being born. Sarah wasn't having it. Casey was sure Sarah wasn't in there anymore. Chuck went off comms and steered them elsewhere. Ellie then notices something.
ELLIE: If you can remember, if you were still you, then you'd want me to do anything to save Chuck. You would want this.
The this? Ellie crashes head-first into a car and knocks the unbelted Sarah unconscious.
Chuck grabs the unconscious Sarah and puts her in the Nerd Herder, over Ellie's protests, as she knows Sarah's far worse than Morgan ever was with the Intersect. He thinks Sarah is still in there and is taking her to a place where she'll remember. Ellie calls Casey because she knows where Chuck would take her: the dream home Sarah claimed she wanted. Sarah was convinced it was still an assignment, and Chuck tells her she's right, only she fell in love with him. Sarah says that's what she does to get a mark's confidence, but he tells her about their first real kiss in Chuck vs. the Imported Hard Salami. He told her she grabbed him and kissed him. Then, after a lot of going back-and-forth (a LOT of going back-and-forth, thanks producers), Chuck was sure she didn't love him . . . then she told the drunken Chuck in Chuck vs. the Other Guy she fell in love with him sometime between fixing phones and disabling bombs with computer viruses. He knew if she remembered him, she would remember this nerdy guy who worked at a Buy More could make her happy.
CHUCK: (cuts her loose) So I'm going to give you a choice, right here right now. You can either take a chance on me and we can start over or you can take these glasses you came for . . . and never see me again.
SARAH: This is real. You really love me?
CHUCK: With all of my heart.
SARAH: I'm sorry. I did my job too well, and I have a mission to finish.
Sarah takes the glasses and starts assaulting Chuck. Chuck refuses to fight back. She doesn't care, kicking him down the stairs. She takes out her gun.
CHUCK: You can kill me. I will never hurt you.
And she almost does . . . until she sees the "Sarah & Chuck" etched into the doorjamb.
SARAH: (shocked) I wrote that.
Before she can put the pieces together, Quinn shows up, takes the glasses, and doesn't deny to Sarah he used her. He shoots Sarah, only Chuck steps in front of her and saves her life. Thankfully, he was wearing a vest, and Chuck tells her to run before the police can get her.
CASEY: Where's Sarah?
CHUCK: She's gone . . . Sarah's gone.
As Ellie and Devon take Chuck home, Sarah is packing to run. Casey pays her a little visit and asks her what she knew about him. She said he was unfriendly, unforgiving, and unquestioning about orders. Casey said people would say that about her, which is probably why they never got along. But Bartowski softened both of them up. Casey dropped off an envelope for her. Inside the envelope? A DVD of her mission with Bartowski. Sarah watched every single day of it and saw herself slowly fall for that Nerd Herd repair person. For example:
SARAH: (on video) Day 564, things are calm for once. No missions, nothing really to report . . .except I find myself sitting here, talking to myself because . . . I love him. I love Chuck Bartowski and I don't know what to do about it!
In Echo Park, Chuck heads back to his apartment after talking to Ellie. Sarah finds him in the courtyard.
SARAH: I believe you, I believe everything you told me about us. But . . . the truth is, Chuck, I . . . I don't feel it. Everything you told in our story I . . . I don't feel it.
CHUCK: Right, of course. I wasn't really sure what I was expecting. But what are you doing here?
SARAH: I just wanted to say I'm sorry for everything that happened today. But most of all, I wanted to say goodbye.
She was going after Quinn to get her life back.