"The Mook, The Chef, The Wife and Her Homer" is the first episode of Season 18.
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, saying 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 school bus and drives to school, and Otto blows his chance to rock with Metallica when the combo hitches a ride with Hans Moleman.
A fuming Otto arrives at the 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, which also includes an introverted boy named Michael. However, when Marge drives back to Michael's house, so that Michael can get his math book, it is revealed that his father is Fat Tony.
News of Michael's "family" spreads, and everyone tries to keep their distance from him. Lisa joins a lonesome 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 opponents, attack them. He manages to turn the tables on the hoods, and when they arrive at the Simpson house, Michael invites the family over for dinner.
At Fat Tony's mansion, the Calabreses come 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. Meanwhile, Michael serves souffles to the Simpsons. He then provides them to the mobsters, who love the dish, but are surprised when they find out he made them. The Calabreses laugh at Fat 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 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 evening, Michael invites the Calabreses to the Simpsons' house for dinner, where he tells the that they have won and that he is out of the family business. They applaud his solution, butm end up choking and dying over their own meals. Marge discovers that the food had been poisoned, and Michael appears remorseful. Then, at Fat Tony's mansion, Fat Tony congratulates Michael for his good deeds. Outside the bedroom, Lisa asks Michael why didn't he tell Fat Tony it was just an accident, although she suspects that it was not quite so. Michael tells Lisa, à la Michael Corleone, not to question his work. Michael 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 the door again to reveal Michael playing with his hot wheels cars.