At school, Lisa befriends a boy, who happens to be the son of mob boss. Fat Tony is put out of commission by a rival family, and Homer and Bart get involved with the mob, when Michael, who is nothing like his father, is not interested in the “family business.”
Bart and Lisa get on the school bus, and Bart takes up the only remaining seat, refusing to let Lisa sit with him. Lisa goes to Otto for help, he replies,"Ya know, I can deal with your problem or I can rock out, but I cannot do both." With that, he puts a tape into his walkman and begins singing along with "We're an American Band". Lisa pulls on the cord for his headphones and the walkman falls onto the floor and breaks. Otto is completely upset about not having music and smashes his head into the windshield and cracks. Bart reassures him by saying that they will sing for him. Otto is annoyed by the children's version of old school songs and by the boring music on the radio. While driving, Otto sees Metallica, whose tour bus appears to have broken down. At first he thought it wasn't real and he was on drugs. Then a little dragon appears and tells him that, although he was indeed on drugs, they were really there. He stops to pick them up. Bart hijacks the bus and drives to school, and he misses his chance to rock with Metallica when the band hitches a ride with Hans Moleman who says he used to sleep with Lars's grandmother. Before leaving, Robert tells Otto to never listen to their music again, and they begin to play "Master of Puppets". A fuming Otto arrives to school and spanks Bart. Principal Skinner notices this act of corporal punishment and suspends Otto from driving the school bus (with pay). Otto cries "NOO!!" and Skinner confiscates his beaded seat cover and his gun. Because of this, the parents have to carpool the kids to school, now including an introverted kid named Michael. However, when Marge drives back to Michael's house, who forgot his math book, it is revealed his father is Fat Tony.
News of Michael's "family" spreads, and everyone tries to keep their distance from him. Lisa joins a lonely Michael at lunch, and they become friends. She comes to find Michael is a talented cook, which he claims to be his dream, rather than go into the family business. After school, Fat Tony drives the kids home, but on the way, goons working for the Calabrese family, Fat Tony's rivals, attack them. He manages to slip them, and when they arrive at the Simpson house, Michael invites the family over for dinner. At Fat Tony's mansion, the Calabreses show up unexpectedly for a sit-down during dinner. Fat Tony advises the Calabreses against killing him as his son, Michael, would then take his place and exact a brutal vengeance. Michael, meanwhile, serves souffles to the Simpsons. He then serves them to the mobsters, who love it, but are surprised when they find out he made them. The Calabreses laugh at Tony and leave. Fat Tony admonishes Michael for making him look weak in front of his enemies. Suddenly, an attack helicopter (piloted by the Calabreses) appears at the window and guns Fat Tony down.
At the hospital, Fat Tony lies unconscious, and Johnny Tightlips explains to the other mobsters that, with the boss down, the Calabreses would be trying to finish the job. He tells Michael that he should step up, but when he resists, Homer volunteers to take his place as mob boss. He and Bart proceed to do mafia dirty work, shaking down money from Moe and Krusty. However, Michael notices how this amount of power is turning the two more maniacal, and seeks to put an end to it. One night, he invites the Calabreses to the Simpson's for dinner, where he informs them that they have won and that he is out of the family business. They applaud his decision, but end up choking and dying over their own meals. Lisa discovers the food had been poisoned, and although Michael appears remorseful, Lisa finds out it was intentional. At Fat Tony's mansion, Fat Tony congratulates Michael for defeating their enemies. Outside, Lisa asks Michael why didn't he tell Fat Tony it was all an accident, though she suspects it was not quite so. Michael tells her, à la Michael Corleone, never to question his business. He walks into the next room and is joined by Jimbo Jones, Dolph and Kearney, who shut the door on Lisa a la Godfather. Lisa opens up again to reveal Michael playing with his hot wheels.