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. Every time he gets stabbed, the rating gets higher. In the end, as he collapses dead onto the desk, blood pours down the front to reveal the title, "The Simpsons Halloween Special VIII".

Mayor Quimby generates a great deal of controversy over a "frog's legs" joke he makes about France and he refuses to apologize. Lisa becomes worried that France will launch an attack against them. Homer tries to reassure her by saying that they have a bomb shelter, but it turns out to be a cardboard box in the backyard. So, Homer goes to Herman's Military Antiques to look for a real bomb shelter. He is looking at the Withstand-inator when the French president launches a neutron bomb directly into Springfield.

Homer, completely unharmed, emerges from the shelter and complains to Herman's corpse about the food. On the way home, Homer doesn't take notice to the lifeless town. At a green traffic light, he becomes annoyed because the person in front of him won't go. He gets out of his car and decides to handle things with a "little friendly punching". He punches the driver in the head, mistaking their head turning into dust for a sign that he 'still has it'. He then notices a newspaper headline that tells about the bomb that blew up Springfield, and he seems to be the only person to have survived.

He misses his family, but he quickly gets over his loss and realizes he can do anything he wants. Homer takes this opportunity to dance naked in the church, when he is confronted by a band of Springfield citizens who have become mutants, but they prefer to be called 'freaks' or 'monsters'.

They claim that they want to create a perfect world in which the mistakes of the past will be eliminated. This, of course, includes killing Homer. Homer flees in his car back home with the freaks chasing him in a type of zombie car. Upon arriving home, Homer is greeted by his family, who survived the blast because their house was protected by so many layers of lead paint. Seeing Homer reunited with his family, the freaks see the error of their ways. Ned Flanders hopes they can build a Utopiaan society where freaks and norms can live together in peace. Marge seems to agree at first, but she and the children open fire with shotguns that they were hiding behind their backs, killing all of the freaks. Homer and his family decide to take advantage of the nuclear holocaust and go and steal some Ferrari's.

Homer buys a 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 two creatures. 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 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.

In 1649 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. Mayor 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 Reverend 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 an evil witch. Marge then vows 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 Flanders and Maude Flanders talking about how the witches may eat children, thus tempting them to hunt. 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 Rod & Todd go. Marge remarks that she wishes they hadn't eaten all those children before they got to the Flanders' house. They go to each house, getting goodies in exchange for not eating the kids. But As they fly off, Horatio McCallister says that is how the tradition of Halloween and trick or treating started, with Maude Flanders' quick thinking leading to the Halloween we all know today.

The next year, the whole town is celebrating Halloween. Homer eggs the door of a house from which no candy was received. Lisa points out that it is their house. And When everyone starts laughing at him, he then accuses Lisa of being a witch, prompting the townspeople to start chasing her down the street in the moonlight.