Chuck, who has had all of the government's top secret information downloaded into his brain, is standing in the Buy More parking lot when he sees something and starts running at full speed. A voice over starts with Chuck introducing himself and his new spy life. We flash inside the Buy More where Harry Tang is complaining to Chuck that the current display is done wrong since it has a Large Mart table cloth. Morgan says he will fix it by performing the old magic trick of ripping a table cloth out from under all of the items on the table. This does not work and everything falls off the table. It flashes back to parking lot where Chuck is still running and a voice over keeps explaining his spy situation and introducing the main characters. He is seen chasing Casey, the NSA agent sent to protect him and works at the Buy More, who is chasing some kid through the parking lot. Casey is chasing a shoplifter and Chuck is trying to make sure Casey doesn't hurt the kid. The kid is caught and Chuck prevents Casey from punching him.
After saving the shoplifter Chuck looks across the parking lot to a store called "Wienerlicious" and sees Sarah, the CIA's secret agent guarding him and posing as his girlfriend, over there. He goes into the store to find out what she is doing over there. She is working there as a cover so she can keep an eye on Chuck, who works for the Nerd Herd, at the Buy More. Chuck is worried that there isn't a plan to get these government secrets out of his brain but Sarah assure him that they have a plan. She suggests they go on a "date" that night to discuss the situation further.
At the Bartowski residence Chuck is trying on shirts for his date with Sarah with help from his sister, Ellie. Ellie is upset that Morgan, who is in the room playing video games, has met Sarah but she hasn't. She plans a group meal at the house the following day.
In Washington Sarah and Casey's superiors are discussing how unfortunate it is that the secrets from the Intersect computer have been transfered to an idiot. But they have arrange for Chuck to meet with the NSA's top scientist to try and fix it.
Sarah pulls up in a every nice car to pick Chuck up for their "date." She takes him to the Buy More where they meet Casey and explains that they will be meeting a doctor that worked on the Intersect computer and that this will hopefully lead to getting the secrets out of Chuck's brain. They put him inside the home theater room with a head set, where he will have to see a few images tell the doctor what they are. He isn't, however, allowed to see the doctor for his own safety.
The doctor arrives and is a little confused about why is isn't allowed to see his patient. He starts the test and Chuck starts naming off what the images are. Dog, Hippo, etc, until the "encoded images start and then he starts spouting out government secrets until the test is over. The doctor is shocked that all of the Intersect secrets could be in one mind and then says he thinks he will be able to remove the information from Chuck. Sarah then takes Chuck home for the night. The doctor is seen driving in the desert when a phone in his back seat starts to ring. The car moves behind a rock and explodes.
The next morning Ellie comes in with the news paper and shows Chuck an article about Bryce's death. According to the article Bryce died in a bank robbery. In the desert Casey and Sarah are digging through what is left of the doctor's car when Sarah finds the charred remains of the cell phone that was last seen ringing in the doctor's back seat. She hides this discovery from Casey and leave the site. Casey, on the phone with his Superior, says he thinks it was a CIA job as he watches Sarah drive away.
Back at the Buy More, Casey comes up to Chuck and whispers to him that he can't trust Sarah. But Big Mike interrupts them and tells Chuck he needs to train Casey on how to improve his customer service skills. As he tried to teach Casey he gets a message from Sarah to meet him ASAP. He tries to fool Casey into doing some role playing with Morgan and slips out to meet Sarah.
At the Wienerlicious there is a group of young boys staring at Sarah while she works. Chuck comes in and that scares all of them away. She says he can't have any private meeting with Casey but Chuck says that he said the same thing about her. She shows him the cell phone which he has a memory flash of. The cellphone is an NSA bomb that destroys all biological traces. Sarah describes Casey as a killer and reminds Chuck that he tried to kill both of them just a little while ago.
When he goes back in the Buy More to see Morgan and Casey but things are not going so well. Casey knocks Morgan to the ground. He then grabs Chuck and demands to know what he talking about with Sarah, but then leaves. He crosses the parking lot to the Wienerlicious where they start fighting. A customer comes in and Casey escapes out the back. Back at the Buy More, Lester gives Chuck a computer errand to run. He is driving around when a SUV bumps into his Nerd Herd car. It is Casey. He calls Chuck on his cellphone and reveals that he was the one that called in the house call. Chuck freaks out, thinking that Casey is the one that killed the doctor and now he is going to hill him. Chuck drives off, trying to escape, with Casey close behind him. Casey crashes into Chuck and makes him stop. Casey shows him his wounds from his fight with Sarah and says that she is rogue, that she is the one that killed the doctor and and just tried to kill him.
Sarah tries to call Chuck but Casey convinces him not to answer and they get into Casey's car. A phone starts to ring and they look in the back seat and see an NSA phone bomb and run from the car before it explodes. Casey says that Sarah is "cleaning house" which means she is killing off everyone she has come in contact with. This reminds Chuck that his sister is having Sarah over for dinner that night and he rushes to go save her.
He gets home to find Morgan, Ellie, Devon (Captain Awesome), and Sarah waiting for him. He tries to get them to eat out, some place public so Sarah can't kill them but it doesn't work. Casey appears at the door with quiches and joins the dinner party. As Chuck gets a chair for him, Casey reminds Chuck of a time that Sarah poisoned a group of French diplomats at dinner. Ellie tells Chuck that Sarah had brought desert. He rushes to keep everyone from eating Sarah's desert he makes a awkward toast. When that doesn't stall them very long he tries to do the same trick Morgan attempted at the start of the episode. Except this time Chuck pulls it off and takes the table cloth right out from under the dishes. Everything stays put except the candle in the middle, next to Sarah's desert. Casey bumps the table and the candle falls over and lights the desert on fire. Everyone screams and Chuck rushes it into the bathroom, pours water on it and stomps on it.
Sarah asks for a moment alone to speak with Chuck. She asks him what Casey said about her and he mentions that they think she killed the doctor and are after them. He asks her about the French Diplomats that she killed and she said they were French assassins. She says that she never asked him to believe her but to trust her. She has a epiphany about who might have killed the doctor since neither she nor Casey killed him and leaves the house. Chuck follows close behind and so does Casey. Before they can catch Sarah she is kidnapped by the doctor who everyone thought was dead. Casey and Chuck get into Chuck's car to chase them down. Casey had laced his quiches with microbots. But unfortunately the only person who ate them was Morgan. With nothing to track Sarah with, Casey is ready to give up but Chuck wont quit. He frantically suggests some ideas which Casey agrees with and they find a warehouse where a helicopter is about to take off from.
Chuck is told to stay in the car as Casey goes in to get Sarah and capture the doctor. As Chuck is waiting he sees the doctor come out of a different building than the one Casey went into. He gets out of the car and enters the building he saw the doctor exit from. Inside the warehouse Sarah is chained to a poll. Upon seeing Chuck she tells him that she tells him that he has to leave. He finds her something to pick the lock with right as the doctor comes back inside. Chuck hides from him as the doctor starts to interrogate Sarah about the location of the human Intersect.
When Chuck sees the needle the doctor is about to stick into Sarah he makes a noise that alerts the doctor to his location he tries to run but the doctor stops him. When Chuck sees him he has a memory flash and sees that the doctor has been selling government science to North Korea. This information lets the doctor know that Chuck is the human Intersect and shoots him with a tranquilizer dart. The doctor is planning on selling Chuck to other countries. He drags Chuck onto the helicopter and they take off as Casey finds Sarah and frees her.
In the helicopter Chuck wakes up after he realizes he only fainted from the idea of being shot with a large needle. He sees the tranquilizer gun and grabs it. He tells them to land but the doctor tries to grab the gun from him. Chuck accidentally shoots the pilot with a dart and knocks him out. Chuck and the doctor wrestle and the doctor gets knocked out. Chuck hops into the pilot seat to try and figure out how to land. Back on the dock, Sarah realizes that Chuck is not the one who is flying. Casey calls Chuck to try and figure out a way to land it but Sarah ends up taking over. Telling him to use the controls like they are a video game, because they games were designed after the real Helicopters. With this knowledge, and constant guidance from Sarah, Chuck is able to land the helicopter.
When he gets out of the helicopter he is very pleased with himself but Sarah is very mad at him. Sarah tells him that the things he know are incredibly important and that everything fell apart when he stopped trusting her and didn't follow directions. She says she is not a double agent like Bryce and if Chuck can't trust her then all three of them will go back to Washington and Chuck does not want that to happen. Then Sarah storms off.
The next morning Chuck is preparing to go to Bryce's funeral. At the funeral he sees Sarah there but she leaves without talking to him. Casey is further back talking on the phone to his superior. She says that in six months the new Intersect will be up and running and that after that, Casey will "do what [he] does best" with regards to Chuck.
Chuck goes to see Sarah at Wienerlicious later and apologizes to her. She apologizes as well but not before expressing how important and dangerous everything is. And how without the doctor to remove the secrets he will be doing more spy stuff and have to lie even more to his friends and family. He begrudgingly accepts. Right then Ellie, Devon and Morgan walk into Wienerlicious to try and give the dinner another shot right there.