Chuck Versus the Alma Mater

Professor Fleming is in the lecture hall at Stanford, giving a lesson on subliminal imagery, when he sees a sinister figure enter the class. He hastily calls an early dismissal and flees, grabbing as many papers as he can and calling for help: He had made a copy of intelligence he should not and now someone is after it. Chuck and the team attend a briefing with General Beckman in the Home Theater room of the Buy More, where Chuck is stunned to learn that Fleming, the professor who had him expelled, was working for the CIA. Beckman wants Chuck to use his connection with Fleming to facilitate his extraction, but Chuck declines. Awesome, his frat brothers, and Ellie are preparing for the UCLA/Stanford game and are asking Chuck to come with them, but he again refuses to return to Stanford. However, while cleaning out boxes of memorabilia from college, Chuck flashes on his old student ID.

Chuck confronts Casey as to why he's in the Intersect, but Casey does not know. Chuck agrees to accompany them to pick up Fleming, and though told to stay in the car while Sarah and Casey go inside the safehouse where Fleming is staying, he gets out when the Professor arrives. Fleming is pleased to see Chuck, and teaches him a secret phrase: "Are you coming to the toga party?" to use if he's in trouble. Chuck asks him why the CIA has a file on him. Fleming apologizes, but before he can say more is shot from behind with a crossbow by Magnus Einar, an Icelandic agent. Fleming tries to give Chuck a scrap of paper with a cryptic number code written on it and asks him to give it to Bryce Larkin, but Einar takes it first.

Fleming is taken into surgery, while Sarah and Casey ask about the numbers. Chuck is unable to remember them all, however, and once again declines joining them to follow up on the lead at Stanford. Ellie gives him a copy of Rise and Fall of the Roman Empire that he checked out before being expelled, and while looking at the spine, he realizes that the numbers Fleming gave him was shelving code for a book at the Stanford library. He quickly passes on this intelligence to Casey and Sarah, and realizes that Fleming must have hidden the data in the library, where Chuck and Bryce played games of Gotcha! There was a particular location Bryce used to hide spare darts, but Chuck realizes he has to go there to find it.

Chuck, Sarah and Casey join Ellie, Awesome and his frat brothers at Stanford. Leaving his family at the tailgate party, Chuck and the team head to the school's library, where Chuck finds Bryce's hiding place and the disk. However Magnus has followed them and the three flee from him and his henchmen but are eventually pinned down in a lecture hall, where Chuck discovers the disk contains a list of students recruited by the CIA, including him and Bryce. Chuck escapes out a side door while Casey and Sarah hold off Einar's men. He finds a computer and begins calling in backup from the students on the disc using the code Fleming taught him. Most arrive at the lecture hall with heavy firepower to relieve Casey and Sarah, while another student ambushes and incapacitates Einar before he can kill Chuck.

Back at home, Sarah allows Chuck time to review his file on the disk before confiscating it. In it, Fleming is about to record an interview with Chuck when Bryce enters and reveals that Chuck never got the message. Fleming says that Chuck is ideal for the Omaha Project, and touts his high rate of retention of subliminal information; he further states that, because of the promise Chuck shows, Chuck will be drafted rather than recruited and he will be "in, no matter what." Bryce fears that Omaha, a military project, would destroy his friend and that he's too good a person to be forced into that life. With no other options, Bryce requests that Fleming help him falsify records to show Chuck cheated on his exams, invalidating his test scores and sparing him from recruitment. Chuck realizes Bryce sacrificed his friendship with Chuck to save him, and that, if Bryce got him expelled to protect him, maybe there was a reason for him destroying the Intersect as well. (And Sarah notes that maybe there was a reason he sent the Intersect to Chuck).

Part of the episode is revealed in flashbacks. When asked why Bryce turned him in, he tells him he brought it on himself, even though Chuck did not do what he was accused of. It was Fleming who revealed that Bryce turned him in for cheating. Chuck also recalls when he first met Bryce at Stanford.

Harry Tang has been on a campaign to restructure the store to his own satisfaction. He implements several policies that have become unpopular, including scheduled lunches and breaks. Morgan finds that he and Chuck can no longer share their lunch hour, to which Chuck laments the loss of "Surf and Turf Wednesdays and Fridays." Harry also institutes a "Green" program, but the final straw comes when Harry hijacks the Buy More video wall during one of the employees' competitions—a race to identify as many television programs in a minute as possible—with a universal remote that gives him control of all the TV sets on the wall (which he utilizes to end the game by changing it to a golf match): "One Remote to control them all."

With Chuck away visiting Stanford, Morgan leads a revolt against Harry. The staff decides the best approach is to steal the One Remote. While Anna flirts with Harry as a distraction, Lester steals Harry's locker key and hands it off to Morgan. However, when Morgan attempts to remove the remote he is caught by Harry after Lester tips him off. Harry confines Morgan to "The Hole," where he is forced to deal with angry customers and returns. He calls Chuck and gains the access code to Harry's remote. Morgan locks Harry out, and barters his way out of the Hole.

• Although set at Stanford, filming of the episode — with the exception of stock footage — actually took place on the campus of rival UCLA. The two schools were playing each other in football in this episode.
• Captain Awesome remarks that instead of Stanford he'd rather see UCLA play SC (the University of Southern California), the Alma Mater of series creators Josh Schwartz and Chris Fedak.
• Chuck's old fraternity at Stanford is Gamma Delta Phi.
• The Library of Congress Classification code for the copy of the Rise and Fall of the Roman Empire seen in the episode is incorrect.
• The number on the paper (219 F5U922) given to Chuck by Professor Fleming does not correspond to a Library of Congress Classification code nor a Dewey Decimal Classification number.
• The "One Remote" used by Harry in this episode appears to be a Logitech Harmony 880 or 890 model remote. Since only the Harmony 890 can use RF (as opposed to IR), it is presumed that the remote must be a Harmony 890, as only RF capability would allow such broad-sweeping ability to change channels from a distance.
• The ending of this episode contradicts the story of how Chuck and Jill met that Chuck told at the beginning of "Chuck Versus the Intersect". The pilot describes Chuck and Jill meeting in class, whereas this episode seems to indicate Bryce introducing Chuck to Jill. However, Bryce's introduction of Chuck does not occur on screen, and might not have happened that day, as Bryce says Jill was "on the quad," but might've gone elsewhere by the time the two showed up looking for her.
• When Chuck looks at the lunch schedule you can see that Morgan is listed as a Nerd herder, and Anna does not have a lunch break.

• Chuck discovers that there is a file on him in the Intersect when he flashes on his old Stanford student ID badge.