After stumbling upon some teenage Wiccans, Lisa accepts an invitation to join their coven. Just before Lisa is inducted Chief Wiggum arrives and arrests the three teens on charges of witchcraft; Lisa becomes the chief witness in the trial. Meanwhile, Homer starts to hang out with his new pal Cletus after discovering the slack-jawed yokel makes moonshine and becomes the local moonshine taste-tester.
The Simpsons return from a ski vacation and Bart and Lisa choose to play "Bonk-It!" to pass the time. Homer gets tired of the annoying noises and destroys the game. Unfortunately the game gets stuck in front of the car's brake pedal and Homer can't stop, so they slide on to a frozen lake. Bambi makes an appearance, before getting hit by Homer's car. Cletus Spuckler rescues them from sinking in the water and takes them to his shack. He invites Homer to drink moonshine with his hillbilly friends, while Lisa plays hide-and-seek with Cletus' daughters. Since they can't count and Lisa chooses a very good hiding place, she gets lost. She wanders into the field and discovers three teenage girls, one of whom is named Cassandra, who are practicing Wiccans. Lisa is skeptical of their spells, so she returns with Homer.
The next day Lisa discovers Ms. Hoover has fallen ill with a stomach virus. She asks the Wiccans if they really made Hoover sick. The girls assure Lisa that they'd never hurt anyone, and ask her to join their coven. While researching Wiccans on her computer (on Wiccapedia), Ned Flanders spots Lisa through his window and, in his usual religiously intolerant manner, contacts the authorities. Just before Lisa is inducted into their coven, Chief Wiggum arrives and arrests the three girls for witchcraft. Lisa becomes the star witness in their trial. Half the town suddenly becomes blind and the girls are blamed. Judge Snyder decides that there is no evidence linking the girls to any crime whatsoever and throws out the case. The townsfolk refuse to accept the judge's ruling and form a mob. They take the girls to the river to prove whether or not they are witches by dunking them with a dunking stool constructed by Groundskeeper Willie. As they are about to be dunked in the icy river Lisa appears with evidence showing the reason they were blinded.
It turns out the hillbillies that Homer had befriended all make their own moonshine, and after discovering Homer's ability to taste the home brew like a fine wine they invite him to be a judge at an upcoming competition. When the police go by on their way to arrest the Wiccans the hillbillies think they're coming for them and throw their stills down the hill, spiking the river with alcohol. The tainted water then ran into the reservoir and blinded everyone who drank it.
After the girls are begrudgingly freed by the townsfolk they thank Lisa for her help and she thanks them for helping her be a little less skeptic. Marge thinks they are nice girls but forbids Lisa from ever going near them again.
The end screen music is "Season of the Witch" by Donovan.