The Simpsons and Ned Flanders hold a seance in order to contact Ned's dead wife, Maude. While praying, Bart comes in dressed as Maude's ghost and finds out that Maude's real ghost is behind him, which startles everyone. Homer and Ned admire Maude, but are terrified when she turns into a hideous ghoul. Maude opens up a green book with the white writing "THE SIMPSONS TREEHOUSE OF HORROR" and someone writes "13" on the book in blood.
Homer walksinto the backyard to lie in his hammock. Marge almost immediately sets upon him with a list of chores, Homer replies by saying she made him to many pancakes and has to sleep them off, slyly acknowledging them as being for the church while patting his stomach, however his hammock collapses much to Marges delight, which is only temporary as he buys a new one from a passing vendor, who warns him that it carries a curse. Disregarding this, Homer lies down and discovers that the new hammock can produce clones of anyone who rests on it. He inspects the first clone and notices that it doesn't have a belly button. He begins making and using clones to do all of his chores, which include helping Marge choose an outfit, visiting Grampa to listen to one of his war-related stories, and play a baseball game with Bart, Lisa and Maggie. The clones are soon revealed to be much more stupid than the true Homer. Lisa notes this while they are playing baseball with one of the clones and the clone smashes the car with a bat. When Ned Flanders asks if he can have his chainsaw back, one of the clones picks up the chainsaw and looks at Homer, who nods. The clone misunderstands and brings back Ned's severed head. Horrified, Homer immediately decides to get rid of the clones and the hammock. He bundles them in a truck and takes them to an isolated cornfield. When they arrive, Homer asks if anyone knows the way home; three Homers put up their hands, prompting Homer to shoot the three clones down with a rifle. He then abandons the rest of them, along with the hammock, presuming that none of the clones are smart enough to get anywhere without him. The clones soon use the abandoned hammock to make an army of Homer clones. Among the hundreds of clones, a few 'mutations' (including Homer as he was drawn on The Tracey Ullman Show version of The Simpsons, Homer after gaining 300lbs to get on disability at work, and Family Guy's own Peter Griffin) are seen. The clones attack Springfield and destroy all of its buildings, except for Moe’s Tavern, which reports record business. US army officials gather in the Mayor's War Room, where Lisa thinks of a solution to solve the problem, after getting the idea from Homer, who became upset when he found an empty donut box. She suggests that several helicopters hook gigantic donuts on cables and have the clones chase them into Springfield gorge. The plan is put into action in a parody of the "Ride of the Valkyries" helicopter scene in Apocalypse Now. Upon seeing the large donuts, all the Homers gasp and exclaim,"Mmmmm. Donuts." and begin chasing the helicopters. The helicopters fly over the gorge, luring the Homer clones to their doom. As each clone hits the bottom of the gorge, he replies, "D'oh!", which echoes across the gorge. Later that night, Marge enters the bedroom and soon discovers that the Homer next to her is a clone (he has no belly button). The clone tells her that the true Homer was the first to fall into the gorge. Marge is initially upset, but relaxes when the clone offers her a back rub as Mike O Malley's "Love The One You're With" plays in the background.
Lisa and Bart are at the Springfield Cemetery, mourning the loss of their pet goldfish, Goldie, who had always been there for them between August and October. Lisa inadvertently discovers the grave of William Bonney, a man who was killed at a young age by gun violence. According to his epitaph, he dreamed of a world without guns. In his memory, Lisa starts a gun control crusade, which makes Springfield 100% gun free -all the guns are sold includen Homer's, Bart's and Maggie's guns, even the police no longer possess guns all guns are turned into a playground. The town is now defenseless, causing the corpses of William "Billy the Kid" Bonney and his cohorts, 'The Hole in the Ground' gang to rise from the dead. The gang starts wreaking havoc on the town, until Professor Frink invents a time machine, which Homer uses to go back in time to stop the gun ban and destroy the zombies. Homer tells the citizens of Springfield to shoot at the zombies' graves, causing them to rise up and flee. Lisa feels guilty about banning guns, because sometimes they are the answer. Suddenly, a more futuristic Homer comes in to warn them about guns that have destroyed Earth in the future. He is then shot by Moe, who has had enough of all this nonsense and plans to use Frink's time machine to find some "caveman hookers". An error in this portion of the episode is when The Hole in the Ground Gang started firing after being introduced, Mayor Quimby has no hair.
In an elaborate parody of The Island of Doctor Moreau by H. G. Wells, the Simpsons are going on a trip to "The Island of Lost Souls", where they find Dr. Hibbert running the island's resort. While the family are there, Marge starts to think that something creepy is going on, although Homer largely dismisses her concerns. She investigates and, consequently, she is captured by Dr. Hibbert, who transforms her into a panther. After having violent sex with the new Marge, Homer realizes she has been transformed.
He goes to find a cure for Marge's new state, but encounters Ned Flanders, who has become a cow-centaur who needs to be milked. After Homer reluctantly milks him, Flanders takes Homer to meet other Springfield inhabitants who have also been turned into 'manimals', including Bart (now a spider), Lisa (now an owl) and Maggie (now an anteater who was almost eaten by Lisa, claiming to be playing the lets eat Maggie game, but was stopped by Homer). Homer, initially appalled at what everyone has become (and that they actually prefer it to being human), eventually embraces the concept of being an animal who does nothing but eat, sleep, mate and roll around in its own filth after realizing how well it suits his lifestyle. He enjoys spending the rest of his life as a walrus and living with his transformed family on the island.
Kang and Kodos appear briefly at the end, commenting on how the skull-shaped island looks like their number 4. This is a reference to the Japanese as their number 4 is an unlucky number, as it spells like death.
Simpsons regulars and their animal transformations in The Island of Dr. Hibbert: Willie (Shaggy dog), Frink (Turkey), Marge (Panther), Ned (Cow), Mrs. Krabappel (Hyena), Jasper (Goat), Selma (Elephant), Patty (Lion), Snake (Skunk), Krusty (Lion), Apu and the octuplets (Possums), Lou (Cheetah), Eddie (Dog), squeaky-voiced teen (Donkey), Rev. Lovejoy (Coyote), Ralph (Peacock), Comic Book Guy (Ram), Grampa (Rooster), Quimby (Panda), Sideshow Mel (Lemur), Manjula (Antelope), Chalmers (Bear), Moleman (Turtle), Moe (Toad), Cletus (Sloth), Otto (Camel), The Rich Texan (Buffalo), the Wiggum Couple (Pigs), Smithers (Flamingo), Luigi (Guinea pig), Bart (Spider), Maggie (Anteater), Lisa (Owl), Wolfcastle (Rabbit), the Captain (Alligator), Dr. Nick (Squirrel), Judge Snyder (Hippo), Mr. Burns (Fox), Bumblebee Man (Bumblebee), Disco Stu (Shrew), Kent Brockman (Rhino), Martin (Sheep), Agnes and Seymour Skinner (Kangaroos), Nelson (Wolf), and Homer (Walrus).
Marc Wilmore, Brian Kelley and Kevin Curran wrote the episode. This is the first Halloween episode to use digital ink and paint as a proof of concept, which led to the decision to have the whole show's animation converted from traditional cel to digital ink and paint.