A Fox censor named Fox Censor, sitting at his desk reading through the script and deleting things, proudly announces that thanks to his editing tonight's Simpsons episode is rated TV-G. But as he says this, a hand with a sword appears out of the on-screen rating icon and stabs him in the back repeatedly, raising the rating with every stab, (TV-PG, TV-14, TV-MA and TV-21). As he collapses dead onto the desk (the final rating was an impossible TV-666), blood pours down the front to reveal the title, "The Simpsons Halloween Special VIII".
Mayor Quimby generates a great deal of controversy after making an offensive joke about France involving the phrase, "frog's legs." When it becomes obvious that no apology is forthcoming, the French president launches a neutron bomb directly into Springfield, passing by Kang and Kodos' spaceship. Homer had been inspecting a bomb shelter he was considering buying from Herman and after the blast; Homer emerges from the shelter to find that he seems to be the only person in town to have survived. He misses his family, but he quickly gets over his loss and, being the last man alive in Springfield, decides to do as he pleases, such as watch a David Spade/Chris Farley comedy in an empty theater and dance naked in church to the song "War" by Edwin Starr. Homer is soon confronted by a band of Springfield citizens who have become mutants. They claim that they want to create a perfect world in which the mistakes of the past will be eliminated. This, of course, involves murdering Homer. Homer flees and arrives at his home where he finds that his family survived the blast because their house was protected by so many layers of lead paint. Seeing Homer reunited with his family, the mutants see the error of their ways. They hope they can build a Utopian society with the Simpsons, but Marge and the children open fire with shotguns that they were hiding behind their backs. Homer and his family take advantage of being nuclear holocaust survivors by going out to steal Ferraris.
Homer buys a matter teleporter from Professor Frink at his yard sale. Bart asks if he can use it, but Homer refuses. That night, Bart tries to sneak Snowball II into the teleporter and at the same time, Santa's Little Helper jumps in. As the pets come out, Santa's Little Helper and Snowball II have been merged into a two-headed creature similar to Catdog. A fly lands on Bart's arm and thinking that he will become a superhero, Bart grabs the fly and steps into the teleporter. He comes out his normal head, but with the body of the fly and meanwhile the fly has his body. The rest of the family wakes up and sees Bart's body with a fly's head and decide that it must be Bart and accept him as their family. That night, Bart the fly talks to Lisa and tells her what happened. When Lisa is in the kitchen fly-boy eats Bart and Lisa knocks him into the teleporter. Bart then appears in the living room normal. An enraged Homer grabs an axe and starts chasing Bart around for using the teleporter.
The year is 1649 and the town of Sprynge-Fielde is witness to many witch burnings. Later in the church, the townspeople try to figure out whom to condemn next. People start accusing others and soon they erupt into chaos, until Marge intervenes. She tries to talk sense into the townspeople, but Moe accuses her of being a witch. Quimby assures her that she is entitled to due process which means she will be thrown off a cliff with a broomstick; if she is a witch she will be able to fly to safety, in which case the authorities expect her to report back for punishment. If she is not a witch, then she will fall to an honorable Christian death. Lisa tries to speak on her mother's behalf, but to no avail and Marge gets shoved off the cliff by Wiggum's henchmen. As Lovejoy speaks to the mob about having done the Lord's work, they hear a cackle and all look up, stunned to see that a green-skinned Marge is flying on the broomstick, as she really is a witch. Marge then takes revenge on the town. She returns to her elder sisters Patty and Selma in their mountain lair close to Sprynge-Fielde. The sisters watch Ned and Maude Flanders talking about how the witches may eat their children, thus giving them the idea in the first place. The three set off for Sprynge-Fielde on their broomsticks. They knock on the Flanders' door and demand the kids. They put the kids in sacks and are about to leave, when Maude offers the witches gingerbread men instead. The witches like these better than the kids and let Rodd & Todd go. They go to each house, getting goodies in exchange for not eating the kids (although they reveal they had already eaten other children before going to the Flanders' house). As they fly off, the Sea Captain says that is how the tradition of Halloween started, with Maude Flanders' quick thinking leading to the Halloween we know today. The scene then jumps to years later in the same village where everyone is dressed in costumes. Lisa ridicules Homer by saying that the house he is throwing eggs at is their own house and because of that he accuses her of being a witch and the townspeople chase her into the moonlight.