Mrs. Krabappel announces that a school-wide Medieval Festival will take place on Friday. Krabappel chooses Lisa to play the Queen, and Bart to play the village cooper, whose job it is to make barrels. Bart isn’t happy with the assignment. Skinner chooses Willie to play the village idiot, and hands him some urine-soaked rags to wear. Willie isn’t happy, either. On Friday the students gather in the gymnasium, which is decorated to look like a medieval castle. As the children feast on turkey legs, Lisa orders Bart to fill everyone’s glasses with pink lemon ale. Bart carries a poorly made barrel into the room. Lisa pats the barrel, which falls apart and douses Bart with a pink liquid. Later a vengeful Willie wheels a giant pie into the gym. As Lisa cuts into the pie, dozens of rats scurry out. Children flee in terror. Milhouse opens his mouth wide, and rats pile in. A chuckling Bart rolls past Skinner on a barrel. Furious, Skinner grabs Bart and blames him for the fiasco. Skinner expels Bart from the school. Bart is so shocked his mouth drops open… and rats scurry in. Fat Tony recommends that Bart be sent to Saint Jerome’s Catholic School. Lisa points out that Catholic schools are usually the most affordable private schools around. Marge decides to send Bart to Saint Jerome’s. During his first day Bart learns that Sister Thomasina uses a yardstick to mete out punishment to misbehaving students.

Bart befriends a cool young priest named Father Sean, who says that he too was once a hellion like Bart, until Saint Peter appeared before him and set him straight. Father Sean hands Bart a comic book called Lives of the Saints and sends him on his way. Bart warms up to Catholicism when he realizes he’ll get to read comics and paint gross pictures of Joan of Arc burning at the stake. Homer, however, grows concerned about Bart joining “the world’s craziest psycho cult.” He rushes to the church and confronts Father Sean. Homer is won over when he realizes that Catholics eat pancakes, drink beer, and play Bingo. Homer is also intrigued when he finds out that Catholics can be absolved of past sins if they repent. Homer makes his way to a confessional, where he lists every sin he ever committed. When he finishes, he cheers, certain he’s cleansed his soul. Father Sean tells Homer he can only be absolved if he’s Catholic. When Homer returns home he tells Marge about his experience. Marge forbids him from joining the church, as she’s against the idea of having more children and letting incense ruin her clothes. When Marge attends church, she shows up without Homer or Bart. Both Flanders and Reverend Lovejoy are against the idea of losing them to “a pointy white hat.” Reverend Lovejoy tells Marge that a different faith means a different afterlife. Marge fantasizes what it would be like spending eternity with fun-loving Catholics instead of austere, preppy Protestants. When she envisions Homer and Bart tossing Jesus into the air on a blanket, the fantasy ends. Flanders assures Marge that Protestants will save Homer and Bart from the Catholic Church. Marge, Flanders, and Lovejoy spy on Father Sean as he tells Homer about making first communion. They burst into the room and drag Bart into a van labeled, “The Ministry Machine.” The van pulls away as Homer and Father Sean burst through the doors of the school.

Homer phones Marge and demands that Bart be returned to the church. Marge tells Homer she’s going to show Bart that Protestants can be just as hip as Catholics. The van stops at the Protestant Youth Festival. Bart is won over when he realizes he’ll get to play paintball. A short time later Father Sean and Homer roar onto the fairground on a motorcycle. Brandishing paintball guns, Flanders and Lovejoy tell Father Sean and Homer to leave. Bart addresses the crowd, reminding everyone that they’re all Christians. Father Sean shakes hands with Flanders, and all is forgiven. Homer says that to keep the family together, they should all go to the same church. Father Sean hopes that everyone learns from Bart’s message of tolerance and understanding. The scene shifts to a thousand years in the future, where armies go to war over Bart the Prophet.