This is exactly the normal opening sequence, except Bart writes "The Simpsons Halloween Special IX" on the board with blood once. Bart trips over Homer's car, and dies where Marge parks. Lisa trips over Bart, getting her head stuck in the wall above the garage door and dies. Marge loses control because of hitting Lisa's legs, so she crashes into Homer, killing him. At the couch, Freddy Krueger asks Jason Voorhees where the Simpsons are; Jason responds: "Eh. Whaddya gonna do?", and turns the TV on, watching with Freddy.

Snake is arrested for smoking inside the Kwik-E-Mart. Chief Wiggum explains that this is Snake's third strike, so he will be executed in accordance with the three strikes law. Before hauling Snake away, Chief Wiggum points out that Apu, Moe, and Bart are all witnesses; Snake vows to kill them all.

After the execution, which happens on live TV, Homer visits Dr. Nick, who transplants Snake's hair onto Homer's head. When Homer goes to sleep the following night, it plants its roots in Homer's brain. With the hair controlling his mind, Homer murders Apu and Moe. Bart realizes that the other two witnesses have been killed, and Homer vows to protect him. Homer locks himself and Bart in a room, but Snake's hair takes control of him. Homer tries to kill Bart with a sledgehammer. Bart begs Homer to fight the hair. After a struggle, Homer rips the hair off his head. However, the scalp comes to life, attempting to suffocate Bart whilst Homer ineffectually punches it, if anything hurting Bart. Wiggum bursts in and shoots the hair dead, then wryly comments on how it has been "a bad hair day", causing everyone to laugh. Marge tries to remind everyone about the two murders, but then suddenly gets the pun and joins in.

Marge forbids Bart and Lisa from watching the Itchy & Scratchy Halloween special while she goes trick-or-treating with Maggie, removing the batteries from the remote control. When Marge leaves, Bart finds plutonium in Homer's toolbox and hammers it into the remote's battery slot. When they use the remote, the kids enter the world of Itchy and Scratchy, and begin to laugh at their antics, angering the cat-and-mouse duo, who proceed to hunt them to teach them a lesson. Both groups even pass by Poochie at one point.

Back in the Simpson house, Homer enters the living room and watches the show. Oblivious to what he sees, Homer decides to change the channel and Bart, Lisa, Itchy, and Scratchy wind up on Live with Regis and Kathie Lee. They disrupt the cooking segment of the show with Regis Philbin and Kathie Lee Gifford causing Kathie to call it a day while stating that Dom DeLuise can interview himself. Then Bart, Lisa, Itchy, and Scratchy end up back at Itchy's house. They urge Homer from inside the TV to use the remote to get them out, and he eventually succeeds just as Marge and Maggie arrive home.

Unfortunately, Itchy and Scratchy also escape. At first, the family is terrified, but soon realize how small the pair actually are, and decide to keep them as pets. After seeing Scratchy fall in love with Snowball II, Marge decides to have him neutered, much to his horror.

Marge discovers Maggie's first baby tooth, which appears to be a sharp fang. Maggie later loses her legs and sprouts her green tentacles. Maggie's pacifier sucks contact the alien duo Kang and Kodos. They arrive at the Simpson house, coming to retrieve Maggie. Marge reveals that Kang is Maggie's real father and explains how it happened.

Kang and Kodos demand that the Simpsons give Maggie to them, but Homer refuses which starts a big fight between Kang and Homer until Bart suggests that they appear on The Jerry Springer Show to resolve their issues. When an audience member criticizes Kang, he vaporizes her, as well as the rest of the audience and the film crew. Everyone looks guiltily as host Jerry Springer does a monologue encouraging them to put their differences aside and do what is best for Maggie. However, Maggie attacks Springer, killing him, causing Kang and Homer to fight again, much to Marge's embarrassment.

After leaving the studio, Kang and Kodos threaten to destroy every politician in Washington unless given Maggie. Marge slyly implies that the aliens could not possibly destroy every politician, and they fly off to do so. As the Simpsons prepare to head home, Maggie says in Kang's voice that she will drive, and laughs diabolically before stating that she needs blood as the credits begin.