Traditional horror movie characters such as Frankenstein's Monster, the Mummy, the Wolf Man, and Dracula roam the streets of Springfield on Halloween night. After they are teased by Dolph (dressed as Venom from Spider-Man), Jimbo (dressed as Master Chief), and Kearney (dressed as The Joker), they get new, more modern costumes from a Halloween store (Dracula as Iron Man, Frankenstein's Monster as SpongeBob SquarePants, the Mummy as Jack Sparrow, and the Wolf Man as Harry Potter).

They then go to an adult Halloween party thrown by Homer (dressed as Zorro) and Marge (dressed as Catwoman), but are soon confronted by their wives (who are just feminine versions of the classic monsters), who are angry that their husbands lied about going to kill children. Homer tries to intervene as the wives begin to assault their husbands, only to be decapitated. Homer's head falls into a bowl of punch when an "X" appears on each of his eyes. "Treehouse of Horror" appears over his eyes that read "XX", summing up to "Treehouse of Horror XX", the title of the episode.

This segment is shown in black and white. After being sent to detention by Ms. Hoover for disrupting class as she claims another student topped her through a tutor, Lisa wants revenge. Bart hatches a "criss-cross" plan and tells Lisa that if she pulls a "ding-dong ditch" Mrs. Krabappel, he'll do the same to Ms. Hoover. Lisa thinks this means ringing the bell at Mrs. Krabappel's apartment and leaving. However, Lisa soon learns that Bart meant for her to kill Mrs. Krabappel, as he has killed Ms. Hoover.

Bart attempts to coax Lisa into killing Mrs. Krabappel with a paper cutter, but she relents. She then tries to kill Bart with a knife after she is shown Skinner's decapitated head, beginning a chase sequence parodying several Alfred Hitchcock films, particularly Spellbound and Strangers On a Train (complete with a Hitchcock cameo and the music from North by Northwest). Bart finally finds shelter at a crowded playground carousel, but is left at Lisa's mercy when the other children leave to get ice cream. Lisa, however, says she'll never be a murderer, and attempts to throw the knife away. It cycles over, though, and impales Bart through the forehead. Lisa and Mrs. Krabappel walk away smiling.

Krusty the Clown introduces a new version of his Krustyburger, the Burger2, made from cattle that have eaten other cattle in their feed. Upon eating a burger on live television, Kent Brockman becomes undead and begins biting everyone around him, triggering a zombie apocalypse. Twenty-eight days later, Springfield has become overrun by "munchers", with the Simpsons being one of the few survivors. Bart, tired of eating fruits, escapes from his family's barricaded house and eats one of the burgers, but turns out to be immune to its effects. The Simpsons are attacked by the munchers after a failed attempt to sneak out, almost being saved by Rainer Wolfcastle, who is eaten by the munchers. They were saved by Apu, driving an armoured off-road truck.

The group tries to leave Springfield, but Apu winds up crashing the truck over a pile of smashed cars. After Apu gets killed, the Simpsons drive on but run out of gas, walking the rest of the way to a so-called "safe zone." During their journey, Homer is bitten by a zombie Mr. Burns, thus turning him into a zombie himself. The family decide not to kill him in the hopes of finding a cure. They reach the safe zone, where Bart being immune to the zombie virus is worshipped as the "chosen one". However, the people there believe that cannibalizing Bart will save them from the virus. The Simpsons, however, think of another solution: vaccinating the remaining populace by having Bart bathe in their food before eating it, thus saving Springfield.

In Broadway musical style, Moe is lonely and upset that he doesn't have a girlfriend and is jealous when he sees Homer and Marge together. When Homer falls into the basement of the bar and is impaled by pipes, his blood becomes the secret ingredient in Moe's new beer. Everyone loves this new beer, saying that it makes them feel warm, secure and cozy on the inside. Moe uses this to his advantage and woos Marge, tricking her into thinking that Homer walked out on her because he's gay.

Homer emerges, alive, despite being impaled by Moe's microbrew machine and hurls Moe across the room (or rather a dummy of Moe), and gets back together with Marge. At the end, the entire Simpsons cast comes out, singing to the audience (including Kang and Kodos) hoping that they enjoyed this episode to the melody of the main theme song. This was the first time in the history of the series that lyrics were adapted to the theme melody.