This is the normal opening sequence, but with a horror motif. Bart writes "The Simpsons Halloween Special IX" on the blackboard with blood and runs out the door. In the driveway, Bart falls off Homer's car while on his skateboard, and dies in the middle of the driveway. Lisa crashes into Bart, flying into the air and getting her head stuck in the wall above the garage door and dies. Homer gets out of his car, sees Marge's car coming, and screams as usual. However, Homer isn't quick enough to get out of Marge's way, so she crashes into Homer, killing him. Marge and Maggie are also killed when the car hits the wall. In the living room, Freddy Krueger and Jason Voorhees are sitting on the couch. Freddy Krueger asks Jason Voorhees where the Simpsons are, and Jason Voorhees responds, "Eh. Whaddya going to do?" (despite the fact that he normally never talks), and turns the TV on, watching with Freddy Krueger.
In a parody of the 1989 horror film, Shocker and the Amazing Stories episode, Hell Toupee, Snake is arrested for smoking inside the Kwik-E-Mart. Which Chief Wiggum explains that after burning down an orphanage and blowing up a bus full of nuns (Snake claims that it was self-defense) where this is Snake's third strike, so he will be executed in accordance with the three strikes law. Before hauling Snake away, Chief Wiggum helpfully points out that Apu, Moe and Bart are all witnesses; Snake threatens to kill all of them. Snake is executed in the electric chair on World's Deadliest Executions, hosted by Ed McMahon and proudly broadcast on Fox. Chief Wiggum then sends the body to the hospital to be carved up for organ donations. Shortly afterwards, Homer visits Dr. Nick Riviera, who gives him a transplant of a full head of still-smoldering hair. The hair is Snake's, and 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 by stuffing him in his own Squishee machine. Homer later removes Moe's heart with a corkscrew and leaves him slumped facefirst in a bowl of Penicill-Os cereal. Bart realizes that the other two witnesses have been killed, but is shocked when his own father comes after him. He begs Homer to fight the hair and, after a struggle, Homer rips the hair off his head. The hair tries to smother Bart and then, as Wiggum bursts through the door with Eddie and Lou, jumps toward the window. Wiggum opens fire and the hair is riddled with bullets and is thus used as a blanket by Maggie, and the story closes with Wiggum remarking, "Now That's what I call a bad hair day!"
In a parody of Stay Tuned, Marge forbids Bart and Lisa from watching the Itchy and Scratchy Halloween special, even though going to the lengths of taking the batteries out of the remote control. They refuse to go trick-or-treating with Marge as Homer is dressed as a hobo and Maggie is dressed as a pirate. But when Marge goes, Bart finds a small piece of highly unstable plutonium in Homer's toolbox and hammers it into the remote's battery slot. When they use the remote, the kids actually enter the world of Itchy and Scratchy. They watch Itchy decapitate Scratchy when he trick or treats at his house and use his head in the manner of a Jack-o-lantern. While the two laugh, Scratchy's head asks why Bart and Lisa are laughing to which Itchy replies that they are laughing at his misfortune. Scratchy re-attaches his head to his body, declares what the duo did was very mean, and forms a partnership with Itchy to "teach them a lesson they will never forget". Where they then throw deadly objects at Bart and Lisa. But as they try to escape, the hated character Poochie passes by, but he is run down by their car. They escape from the car, and wind up on Live with Regis and Kathie Lee in a pot of soup because Homer changed the channel. Bart and Lisa return to Itchy and Scratchy's house when he changes the channel back. Lisa urges Homer to press the "exit" button, which gets her and Bart (whose body was devoured from the neck down by piranhas, leaving only his skeleton) out of the television. She presses the "rewind" button on the remote to restore Bart's flesh, but unfortunately, Itchy and Scratchy smash through the screen. However, they emerge the same size as their real animal equivalents, and they are therefore harmless. Homer decides to make Itchy a pet, and Snowball II falls in love with Scratchy, which however, Marge decides to neuter him, causing Scratchy to scream while covering his crotch.
Marge discovers Maggie's first baby tooth, which appears to be a sharp fang. Maggie later loses her "baby legs" and grows green tentacles. Marge decides to take her to Dr. Hibbert, who prescribes "Fire, and lots of it!" after Maggie crunches his equipment with her fang. At home, Maggie loses her arms too, and it is found that she can contact somebody by sucking extra-rapidly on her pacifier, which appears to be 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 retells the story: Kang and Kodos abducted her while she was doing laundry, selecting Marge for a cross-breeding program. She says the aliens used mind-control techniques on her (Kang simply pointed and said "Look behind you!" before zapping her with an insemination ray). She recalls that nine months after the abduction, Maggie was born. Kang and Kodos demand that the Simpsons give Maggie to them and a struggle ensues. Both Homer, Marge, and aliens start to fight over Maggie until Bart (who is angered by this) stops them and suggests that there can be only one way to solve the problem: let the Simpsons appear on The Jerry Springer Show, with Homer and Kang fighting it out. Then when they appear to discuss things, Kang uses his ray gun to vaporize an annoying audience for criticizing him. During Jerry's "final thought" Maggie attacks Jerry and kills him while Homer and Kang resume fighting.
Jerry, Homer and Kang swear a lot in the process with Marge swearing once to express the humiliation of it all. Kang and Kodos now threaten to kill every American politician unless the Simpsons give Maggie to them. Marge and the Simpsons slyly imply that the aliens couldn't possibly kill every politician, and as they fly off to do so, Bart reminds them not to forget Ken Starr. Just when they're about to leave, Maggie takes out her pacifier and tells everyone in an alien voice "very well then, I'll drive! Ha ha ha! I need blood!".
This episode was nominated for the 1999 Emmy Award for Outstanding Music Composition for a Series (Dramatic Underscore).
List of the Halloween names used by the staff on this episode:
RAT GROENING VEINS HELL BROOKS MATT GROIN INJURY SAM "SAYONARA" SIMON, RICHARD WRESTLING SAKAI
DOMIQUE FAVORITE SWEETER GHOULIE KAVNER NANCY "KILLER ACTOR" CARTWRIGHT THE CANKER, YANK MY AREA HARRY (DEAD TIL 2005) SHEARER
The original version of "Hell Toupee" was supposed to have Troy McClure host Snake's execution, but since the voice of Troy McClure (Phil Hartman) unfortunately died, the entire sequence was redone with Ed McMahon as the host, with McClure's usual introduction reworked for McMahon ("Hi, I'm Ed McMahon. Tonight on Fox, from the producers of 'When Skirts Fall Off', and 'Secrets of National Security Revealed'..."). The Troy McClure version has never been aired on TV.
This episode was the first episode opening to feature Homer actually being hit by Marge's car. The updated opening starting with Season 20 began showing Homer being hit by Marge's car (though obviously without him being killed.)