In Send in the Clones, Homer ends up cloning himself and begins wreaking havoc in Springfield. In The Fright to Creep and Scare Harms, Lisa rallies the removal of all the guns in Springfield. These leave the town defenseless against a menacing force. And finally the Simpsons find themselves at the bay of an evil Dr. Hibbert in The Island of Dr. Hibbert.
The Simpsons and Ned hold a seance in order to contact Ned's dead wife, Maude. While praying, Bart comes in dressed as Maude, but everyone's focus shifts to Maude's ghost. Ned is happy to see his late wife again as she still looks pretty the same since he buried her the day she died, but then Maude appears as a ghoul which scares everyone. She cackles evilly and she opens up a green book with the white writing "THE SIMPSONS TREEHOUSE OF HORROR" and the number "13" drools on the book in blood as Homer screams repeatedly as the episode goes into the first story.
In a parody of Multiplicity, Homer walks into the backyard to lie in his hammock. Marge sets upon him with a list of chores to do for the day. Homer is reluctant, but his concern changes to getting a new hammock because his old one breaks. A man selling hammocks sells Homer one with a fancy design, but he warns Homer that the hammock can cause trouble. Disregarding this, Homer lies down and discovers that the new hammock can produce clones of himself. He begins making and using clones to do all of his chores.
One day, when Ned asks if he can have his chainsaw back, one of the Homer clones picks up the chainsaw and looks at Homer, who nods. However, 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.
In the cornfield, 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, King-Size Homer, smart Homer (HOMЯ) 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 after they learn the clones will encompass the entire United States if not stopped, 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, and upon seeing the large donuts, all the Homers begin chasing the helicopters. The helicopters fly over the gorge, luring the Homer clones to their doom.
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 real Homer was the first to fall into the gorge. Marge is initially upset, but relaxes when the clone offers her a back rub as Stephen Still's "Love The One You're With" plays in the background.
In a parody of The Terminator, Lisa and Bart are at the Springfield Cemetery, mourning the loss of their pet goldfish, Goldie. 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. 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".
In a parody of The Island of Dr. Moreau by H. G. Wells, the Simpsons are going on a trip to "The Island of Lost Souls." On the island, 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, 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). 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, intending to spend the rest of their days on Dr. Hibbert's resort. Meanwhile the two aliens Kang and Kodos appear, commenting on how the skull-shaped island looks like their alien number 4.
Characters and their animal transformations in The Island of Dr. Hibbert:
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.