The scene opens with Chuck worried about Sarah. Morgan and Casey tell him that hacking in the CIA wasn’t good, but are with him 100%. However, when they open the door, Sarah is there. The scene flashbacks with Sarah’s handler, Quinn, telling her about her mission. He says that it is to kill Chuck. He asks her if she has any questions and she asks him why she should believe him and they begin to fight. The man says that he is on her side, but she manages to toss him through the window. Back at Chuck’s, Sarah tells Chuck, Morgan, Casey, Devon and Ellie that the chip is out of her head and that it is all over now. Ellie suggests that she rest now. However, she is listening to Quinn on the other end. The scene flashbacks with Sarah throwing Quinn through the window and hangs him out the window. He says that he has something to show her. He shows her a video recording of herself talking about the mission that she is to do. Quinn tells her that Chuck is responsible for the deaths of two people and that she needs to get the special glasses that Chuck is using to repair Intercept. She has her mission details. She has to kill Chuck.
Sarah cuts chicken and Chuck is impressed that she is violent when she is cutting it. He leaves and Sarah looks around for the glasses. Chuck calls Morgan and says that she seems different. Morgan says that she has been through a lot and that he needs to help her relax. He goes out of the bedroom and finds Sarah with his Darth Vadar helmet. He tells her to meet him in the bedroom. Sarah thinks that he is on to her and her handler says that she needs to be prepared. She opens the door and Chuck roleplays and says that she is there for a Spa treatment and massage. He leaves to let her get out of her clothes and she searches around. Her handler tells her to go along with it. He comes back in and Sarah hides a knife under the pillow. He tells her to relax, but she says that she would like to go to bed. Morgan goes up to Casey and tells him that he can’t believe how things are and that they have no more missions. Casey says that he hasn’t changed like Morgan thinks. Ellie and Devon are at home and they both get letters for positions at a Medical Center. They realize that this could get them a big house and that it is worth it. Ellie has second thoughts because she wants to be close to Chuck. Devon says that Sarah is back and that Chuck will be alright.
Meanwhile, Sarah and Chuck are in bed and she gets up and finds the glasses that her handler was talking about. She gets back in bed and Chuck offers his feet to her. However, she turns them away. Chuck gets up and goes over to Ellie’s place. She answers the door and he asks to come in. Sarah follows him, knife in hand. Chuck tells Ellie that he is going to sneak into the CIA and plant a virus to destroy the Intercept. Sarah hears this and her handler tells her that she is going to have to protect the Intercept and Sarah overhears that Chuck was upset that Sarah didn’t wrap her feet around his. Chuck leaves and goes back into the room. Sarah is already back in bed and she complains that she is cold. She wraps her feet in his and snuggles up. The next morning, Chuck talks to Casey, Morgan and Sarah. He tells them that they need to destroy the Intercept. They all get on board for their last mission. Chuck goes through Sarah’s bag to find contacts, but instead finds the glasses that she took. They arrive at the CIA lab and Morgan sees that the scientists are have invented an Invisibility Cloak. Right away he starts to quote Harry Potter and Casey gets upset with him and tells him not to mess around with anything.
They get to the main section and Casey says that there are 4 guards. Sarah jumps through the window and starts taking out the guards one by one. Chuck is impressed and a little frightened as well. She lets them in and they go to the lab where the Intercept is. Sarah takes the glasses out of her bag and downloads the Intercept rather then the virus. She gets up and puts a gun to Morgan’s head. She tells Casey to drop his gun and Chuck goes up to Sarah and tells her that she isn’t like this. They realize that Quinn has gotten to her and says that she isn’t following the right orders. She punches Chuck and leaves trapping them inside the room. She puts an explosive to the wall and leaves. Casey realizes that she put an explosive device on the wall and Chuck can’t believe that she would do that. Outside, Sarah has second thoughts of detonating. Quinn doesn’t care and detonates it himself.
Chuck, Morgan and Casey climb out of the rubble. They are safe from hiding in the floor ducts. Meanwhile, Sarah pulls up to Quinn and punches him in the face and tells him that was for blowing up the government building. He says that Chuck is better dead. She gives him the glasses and sees that they are fake. She tells him that Chuck must have switched them when he tried to convince her not to go. Chuck calls and Quinn and Sarah realize that he is still alive. She promises Quinn that she won’t fail him again. Casey and Morgan are upset that Sarah got the latest version of Intercept. However, Chuck shows Morgan and Casey that Sarah didn’t get the Intercept because he switched out the glasses. He can’t believe that she would do this. Chuck says that Sarah is not gone and Casey tells him that she is a trained assassin and that she could go after Ellie and Devon. Chuck calls Devon and he says that Ellie went to have coffee with Sarah. Ellie and Sarah are having coffee when Chuck calls. Sarah says that it was a good move to switch out the glasses and tells him that if he doesn’t bring the glasses, then she will kill his sister.
Chuck calls Beckman and she tells him that he needs to make sure that Sarah is lead to a certain point where snipers will be waiting. She tells him that they will do anything to protect his sister. Chuck goes up to Sarah and tells her that he has the glasses secured somewhere. He tells her that he will lead her to the location. Sarah takes Ellie as collateral. They drive and Chuck talks to Casey, who is in position with the sniper rifle. However, Chuck has second thoughts and drives past the meeting point and continues to drive. In the car, Ellie tells her that she doesn’t need to do this. Ellie sees that Sarah doesn’t have her seat belt on and tells her that the “real” Sarah would want her to do anything to protect Chuck. Ellie crashes the car into another car and knocks Sarah unconscious. Chuck pulls up to them and pulls Sarah out of the car. He says that he is taking her to a place where she will remember their relationship. Casey gets a call from Ellie and she gives him the update. She tells him that she knows where he would have taken her. Sarah wakes up and Chuck tells her that they’re at their Dream House and that she has to remember everything. He says that a nerdy guy like him can make her happy. He says that she can either take a chance on them or take the glasses. She says that she did her job too well and fights him.
The fight moves downstairs and she tells him to fight her. He refuses to fight her and she pulls a gun on him. Sarah sees an etching “Sarah + Chuck” on the wall. She remembers it and Quinn shows up and takes the glasses. He tries to shoot Sarah, but Chuck throws himself in front of the bullet. She asks if he is alright and he says that he is wearing a vest. He tells her that they are coming for her and she runs away. Casey comes in and Chuck says that Sarah is gone. They take Chuck home and he morns the fact that Sarah is really gone. Meanwhile, Sarah is packing to leave when Casey comes in and tells her that they should remain friends and that Chuck has made both of them like him. She tells him that Beckman gave him a new assignment and said that he thought that she would want to see something. He leaves and she looks inside the envelope. It is her entire video logs on Chuck. She realizes that she loved Chuck once. At Ellie’s, she asks if he wants to sleep at the house and he says that he will be alright. He says that he loves Ellie. Sarah comes up to Chuck and tells him that she believes him and everything that he told her. However, she doesn’t feel it. He asks what she is doing there and she says that she wanted to say sorry and goodbye. She says that she is going after Quinn. He says goodbye to her and the episode ends.