The Simpson family and Ned Flanders hold a séance in the hope of communicating with the spirit of Maude Flanders. Bart tries to trick Ned by dressing up as Maude's ghost, but the real ghost of Maude, now a demonic spirit, appears instead.
In a parody of Multiplicity, Homer's hammock collapses while he is taking a nap. He purchases 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 does not have a belly button.
He makes clones to do all of his chores, which include helping Marge choose an outfit, visiting Grampa to listen to one of his rambling war stories, and play a baseball game with Bart, Lisa and Maggie. The clones are soon revealed to be more stupid than Homer. One clone kills Ned Flanders by cutting off his head with a chainsaw after Flanders asks if he can have his chainsaw back. Shocked by Flanders' wrongful death, Homer 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. When three clones raise their hands, Homer shoots them, 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 use the abandoned hammock to make an army of Homer clones, many of which are mutations, including The Tracey Ullman Show version of Homer, a faceless Homer, a morbidly obese Homer, a Homer with thick, black glasses, and Peter Griffin from Family Guy. The "clone army" consumes all of Gil Gunderson's crops and Gil himself, then attacks Springfield and destroys all of its buildings, except for Moe’s Tavern, which reports record business. US army officials gather in the Mayor's War Room, and determine that the clones will eat up America by the next day. Lisa thinks of a solution to solve the problem, after getting the idea from Homer, who became upset when he found an empty doughnut box. She suggests that several helicopters hook gigantic, sprinkled doughnuts on cables and lure the clones into Springfield Gorge to their doom. In the end, Marge is shocked to find that the Homer she has is a clone and the real Homer was the first to die due to his obsession of donuts. Marge worries over the real Homer's death, until the clone Homer gives her a backrub.
In a parody of The Terminator, Bart and Lisa 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; even the police no longer possess guns. The town is now defenseless, causing the corpses of William "Billy the Kid" Bonney and his cohorts, "The Hole in the Ground" gang (Frank James, Jesse James, the Sundance Kid (without Butch Cassidy, as they are "not joined at the hip"), and Kaiser Wilhelm II) to rise from the dead. The gang wreaks 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 H. G. Wells's The Island of Dr. Moreau, the Simpsons visit "The Island of Lost Souls", where they find Dr. Hibbert running the island's resort. Marge says there were rumors he has gone mad. The family has dinner with Professor Frink, who is transformed into a turkey as the main course, Marge explores the island, and is captured by Dr. Hibbert. She is then transformed into a blue humanized panther. She returns to her room and has violent, animal sex (literally, scratching all of his back with her claws) with Homer. He realizes that she has been mutated, then asides that he should have realized this during the sex.
Homer treks across the island looking for a cure to Marge's condition, but encounters Ned Flanders, who has been mutated into a cow-centaur, in need of a milking. After Homer reluctantly milks him, Flanders takes him to meet other Springfield inhabitants who have also been turned into mutants, including Bart (now a spider), Lisa (now an owl) and Maggie (now an anteater, who is nearly eaten by Lisa until Homer intervenes). Homer, initially appalled at what everyone has become, eventually embraces the concept of being a mutant animal who does nothing but eat, sleep, mate and roll around in its own filth upon realizing how well it fits in with his personal lifestyle. The segment ends with a contently mutated Homer in the form of a walrus, and the rest of the Simpsons and Springfield mutants lounging aside the resort’s pool, intending to spend the rest of their days on Dr. Hibbert’s resort.
A deleted scene features Homer (as a walrus) giving Marge (as a panther) a back scratch. Marge then coughs up a hairball and Dr. Hibbert immediately begins planning on changing the whole animal hybrids back into humans.
The entire Treehouse of Horror XIII episode concludes with an appearance by Kang and Kodos, observing that Dr. Hibbert’s skull-shaped island resembles their alien number 4.