At school, Lisa befriends Fat Tony's son. Fat Tony is put out of commission by a rival society, and Homer and Bart take over running mob operations, when Michael, who says of being nothing like his father, is not interested in the “family business.”
Bart, Lisa and the other kids are on their way to school when Otto sees Metallica, whose tour bus appears to have broken down. While Otto talks to the band, Bart hijacks the bus and drives to school, and Otto misses his chance to rock with Metallica when the band hitches a ride with Hans Moleman.
An exasperated Otto arrives at school and spanks Bart. Principal Skinner observes this activity of corporal punishment and suspends Otto from driving the school bus (with salary). Because of this misdeed, the parents now 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 dirty mafia business, 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 home for dinner, where he informs them that they have won and that he is out of the family business. They applaud his solution, but end up choking and dying over their own meals. Marge discovers the food had been poisoned, and Michael appears remorseful. At Fat Tony's mansion, Fat Tony congratulates Michael for his bravery. Outside Fat Tony's bedroom, Lisa asks Michael why didn't he tell Fat Tony it was all a mistake, although she suspects that it was not quite so. Michael tells Lisa, à la Michael Corleone, not to question about his work. He then walks into the next room and is chaperoned by Jimbo, Dolph and Kearney, who close the door on Lisa a la Godfather. Lisa opens up again to reveal Michael playing with his hot wheels cars.