After ruining a review by Superintendent Chalmers of Springfield Elementary by playing on Groundskeeper Willie's vehicle while trying to escape being locked up by Principal Skinner for the review, Principal Skinner is furious with Bart and expels him, forcing Marge to homeschool Bart. Meanwhile, everyone in Springfield is excited for Whacking Day, but as the holiday approaches, Lisa condemns it as violent. Whacking Day is a decades-long tradition which calls for the townspeople to beat snakes to death with sticks. Lisa decides to save the snakes with the help of Whacking Day's honorary MC, Barry White, who uses his sonorous bass vocal style to lure the snakes to safety, where no one can whack them.
Principal Skinner lures Bart, Jimbo, Kearney, Dolph and Nelson to a utility basement with the promise of free mountain bikes. When they get there, however, they're informed that they're being "swept under the rug" during an inspection by Superintendent Chalmers. Bart escapes through a ventilation shaft, and then takes Groundskeeper Willie's tractor for a joyride. He quickly loses control, and it ends up hitting Chalmers in the rear. When Chalmers informs Skinner the accident has cost him a promotion, Skinner responds by issuing his harshest punishment yet: expelling Bart.
Meanwhile, Kent Brockman announces that a celebration that was found to be "disgusting and puerile" by a group of hillbillies is coming up. The upcoming celebration is Whacking Day - every May 10, the people of Springfield drive snakes to the center of town and beat them to death. Lisa is appalled at the upcoming Whacking Day celebration, but her protests fall on deaf ears. She tries to appeal to Homer to not lower himself to the level of others, but Homer is set on participating in Whacking Day.
Bart remains expelled from Springfield Elementary, and his parents try enrolling him in a private Christian school. He gets in trouble almost immediately for singing "Beans, Beans, the Musical Fruit" when asked for a psalm, and is chased from the building by the teacher and other students. Marge then decides to homeschool Bart. For one of her assignments, Marge gives Bart "Johnny Tremain" to read, which was a favorite of hers when she was a little girl. Bart gains interest in the book when learning the protagonist was deformed by being wounded in war, and afterwards starts becoming a serious student, even missing an episode of Itchy and Scratchy to read the book. On a "field trip" to Olde Springfield Towne, Bart notices a discrepancy in the Jebediah Springfield story: on May 10, 1775, the day he led an attack on Fort Ticonderoga, he also supposedly founded Whacking Day. At a loss for words, the Squeaky-Voiced Teen in charge of the tour decides to force Bart to leave.
Barry White (who Mayor Quimby introduces as Larry White) arrives to begin festivities, but when he discovers what the holiday is about, he is disgusted, compared to the ignorant joy of the assembled crowd. Bart finds out about the true origin of Whacking Day. He suggests to Lisa that they can lure the snakes to safety by playing music with a lot of bass and putting the stereo speakers to the ground. Homer's record collection, which boasts such gems as Tiny Tim, The Chipmunks, and A Castrato Christmas, leaves much to be desired, but they get some assistance from Barry White (who was conveniently walking by). With White's vocals and Lisa's bass guitar playing, they attract hundreds of snakes into the house to the tune of White's 1974 hit song “Can't Get Enough of Your Love, Babe”.
The crowd arrives in pursuit, but they are soon turned around on the subject of Whacking Day by Bart's newfound knowledge. It turns out that the day was actually invented in 1924 as an excuse to beat up the Irish, a fact confirmed by a fellow Irish man. Mayor Quimby, not knowing that the city has changed its heart, shows up with pre-whacked snakes, but is booed by the crowd while the surviving snakes flee away to freedom. Skinner is impressed with Bart's efforts, and welcomes him back to the school—then realizes in horror that the bullies are still in the utility basement. He races back to the school with mountain bikes for the four bullies still in the basement, hoping that they're all still alive and that he won't have to face any lawsuits from their families; in case the bullies die, he and Willie, who's hauling the mountain bikes with his tractor, will escape to Mexico; Willie mutters under his breath, "I'll turn ya in at the next toolbooth."