The boys are waiting at the bus stop when Cartman notices Stan has a black eye. As it turns out, his sister, Shelly, has been beating him up and he doesn't know what to do. Kyle has problems of his own, as his mom won’t let him keep his new pet elephant (that he got from mail order from Africa) in the house. At school, Mr. Hat teaches the class about genetic engineering, which prompts Kyle to decide to splice his elephant with Cartman’s pot-bellied pig, Fluffy, to make little "pot-bellied elephants". Upon hearing this Terrance bets Kyle that he can clone a whole person before Kyle can get a pot-bellied elephant. Thus, the cloning war begins.
Mr. Garrison suggests the boys use their genetic modifications for the upcoming science fair and that Kyle and crew should check out the genetic engineering ranch outside of town. Mr. Garrison then asks Stan to stay after class to talk about his black eye. When Stan explains that bruise is from his sister Mr. Garrison calls him a pansy and sends him home.
While at the ranch, Dr. Mephesto shows them his genetically engineered collection, including several monkeys with multiple asses. Mephesto then explains that, just like the Loverboysong says, "pig and elephant DNA just won’t splice." He then steals a blood sample from Stan and the boys flee.
Back at school the boys learn Terrance has cloned a human foot. The boys go to Chef with their genetic engineering problem, and after he too cites the Loverboy song, he gives them the idea to try to have the animals "make sweet love" to breed. Stan goes home and gets beaten up by Shelly again.
Meanwhile, back at the ranch, Mephesto and his assistant have created a human clone of Stan for Terrance (Mephesto’s son)'s science project. The boys attempt to get the pig and the elephant drunk to get them to make sweet love, but it doesn’t seem to be working until Chef stops by and sings to the animals with a little help from Elton John.
The cloned Stan breaks free from Mephesto's ranch and proceeds to terrorize the town. The boys eventually find the clone and take it to Stan’s house and persuade it to attack Shelly, which it does after destroying the house and indirectly killing Kenny. Mephesto shows up and kills the clone, but Stan is afraid he’ll be in trouble for everything the clone did, but Shelly, in a brief moment of kindness, takes the heat (after which she beats up Stan again).
When the science projects are due Terrance presents a five assed monkey, but Kyle has nothing until the pig gives birth to a pot-bellied pig that looks like Mr. Garrison. Garrison quickly awards it first prize over Terrance's five-assed monkey.
Comedy Central removed a scene of Shelly repeatedly lighting Stan on fire with matches for fear that the show would come under the same controversy that Beavis and Butt-Head did in 1993 after a little boy set his trailer on fire killing his two-year-old sister "imitating a scene from the show". The scene is not present on the Season 1 DVD set, and in the director's commentary Matt and Trey both can't remember why there's a puddle of water under Stan all of a sudden (from Shelly putting him out with a bucket of water).