Bart and Milhouse go out to spend $50 that Bart won when he bet Homer that he could not eat a spoonful of rotten baking soda that Lisa dug out of the back of the refrigerator. But they get into trouble at the The Android's Dungeon when, after talking Martin Prince's mom out of selling Martin's rare and invaluable Star Wars items to Comic Book Guy for only five dollars, they are banned for life from Comic Book Guy's store.
When they hear that special effects artist Tom Savini is to appear at The Android's Dungeon, they plot to sneak in, but are rebuked at the door. During the interview, Savini repeatedly plays tricks on Comic Book Guy, which causes him to get irate, and as he rages at Savini and everyone else in the comic book store, he suffers a heart attack. Dr. Hibbert tells Comic Book Guy that he needs to take a break from running the store and to leave it in the care of friends. Since he actually doesn't have any friends, Comic Book Guy leaves the store in Bart and Milhouse's care. The store becomes wildly successful under the management of the two boys, only to lose much of its newfound prosperity after Milhouse goes overboard in ordering a shipment of two thousand comics depicting "Biclops", a superhero with thick glasses, which flops spectacularly.
After arguing, the boys unintentionally discover a secret stash of illegal video clips. Bart and Milhouse charge admission for viewing such clips as a "good version" of The Godfather Part III, a clip of Mr. Rogers drunkenly yelling at the director of his show, a secret government plan to use Springfield as a testing zone for nuclear missiles, and Ned Flanders' alerting the police that Homer released a radioactive ape in his house. The scheme works until Chief Wiggum conducts a raid on the store. Despite this, the boys manage to keep the profits from their time managing the store. Meanwhile, Homer has been helping a recovering Comic Book Guy look for a friend, but his attempts fail until he meets Agnes Skinner. Comic Book Guy and Agnes become romantically involved. However one night while they are kissing in bed, Chief Wiggum charges Comic Book Guy for his pirated videotapes. Bart and Milhouse, freed from running the Android's Dungeon, decide that they had fun, but it was time to go back to school. The episode ends with a radioactive ape ordering Ned around.