The Father, the Son and the Holy Guest Star is the 21st and final episode of Season 16. It first aired on May 15, 2005. Liam Neeson guest starred in this episode as Father Sean. It was written by Matt Warburton and directed by Michael Polcino. The episode is the 350th episode produce (in production order) of The Simpsons. Originally slated to air April 10, 2005, it was postponed with no episode playing that night (it was finally aired May 15, 2005) due to the death earlier that week of Pope John Paul II, as the episode revolved around the Roman Catholic Church.
Bart is expelled by Principal Skinner for a prank at a school Medieval Festival that was actually caused by Groundskeeper Willie (who was mad at having to be the village idiot and the one should have been fired), and ends up going to a Catholic school, which is more affordable than other private schools. The only person who takes a real interest in Bart is Father Sean, who explains he acted a bit like Bart in his day, and lends Bart a "Lives of the Saints" comic book. Marge is afraid that Bart is turning into a Catholic (which, with all of the sitting, standing, and kneeling, she calls "Simon Says without a winner"), but Homer is sidetracked by the fact that the school is having a pancake dinner followed by bingo, and when he discovers that he can be absolved of all sins through confession if he converts, Marge problems are doubled, especially when she realizes that Catholics do not believe in birth control. 
Springfield Elementary School is holding its medieval festival. All the students are given roles: Lisa is the queen, Martin is the king, the school bullies are the imperial guards, Bart is the cooper (a role he bitterly hates) and Groundskeeper Willie, against his will, is cast as the village idiot. Bart is mad about his role since it requires him to carry an obscenely large and heavy barrel of pink lemonade around the entire gym and he is treated terribly by everyone, especially Lisa (who makes him trek across the gym several times with the barrel to refill her glass treating him with complete disrespect and has him escorted to the "dungeon" when he mumbles at her under his breath). As much as Bart hates his role, his hatred was not as strong as Willie's. Not only was he forced at the sake of his job to wear a humiliating costume for the fair, but was also forced to sit in a cage in shackles while the students throw rotten fruit at him. For revenge, Willie secretly fills the large pie with hundreds of rats inside. The rats reek havoc on the gym and the entire event falls apart. Due to his history of juvenile behavior, Bart is blamed for the prank instead of Willie and is expelled from school (He is later welcomed back as an apology in the end for being blamed for Willie's prank). At dinner that night, his entire family is upset with him and refuse to believe his innocence. After looking through other schools, Marge decides to enroll Bart in St. Jerome's Catholic School. There, Bart's hip, rebel attitude is frowned upon.
While holding out two dictionaries, Bart meets Father Sean (voiced by Liam Neeson), who came to become Catholic after he was beaten by his father and St. Peter told him to repent. He is sympathetic to Bart and gives him a comic book about the saints and he is drawn into it. At home, Marge becomes concerned over Bart's interest in the Roman Catholic Church. Homer goes to the school to confront Father Sean, but reconsiders after having pancake dinner and playing Bingo. After expansively confessing, Homer learns he must convert to Catholicism to be absolved of his sins. With Bart and Homer both considering joining the Church, Marge (worried she might be alone in Protestant Heaven while Bart and Homer are in Catholic Heaven) seeks help from Rev. Lovejoy and Ned Flanders, who agree to stop them. While they are learning about First Communion, Marge, Lovejoy, and Ned capture Bart.
On the road, Marge and Lovejoy try to bring Bart back to the one true faith: The Western Branch of American Reform Presbylutheranism. Back at the house, Lisa agrees with Homer and Bart's desire to join a new faith. Even after getting laughed at for being Buddhist by Father Sean, she says that Marge is taking Bart to a Protestant Youth Festival. Homer and Fr. Sean then leave in immediate pursuit. At the Festival, Marge fails to bribe Bart with the banal Christian rock of Quiet Riot (Pious Riot after their conversion, possibly a reference to the real life band Pussy Riot). However, he agrees after he plays some paintball, making her happy that "one of those dumb things would work". Homer and Fr. Sean arrive with a motorcycle, shoot Marge's hair with some paintball bullets and engage in a Mexican standoff with Ned and Lovejoy. Bart dismissively tells everybody to calm down and says it's stupid that all the different forms of Christianity are feuding since the main beliefs are the same and there are only a few minuscule difference between them. The two groups agree to both fight monogamous gays and stem cells and to take Bart's idea to heart. The episode then jumps 1,000 years into the future, when Bart becomes the last Prophet of God. In this age, mankind is waging war over whether Bart's teachings were about love and tolerance, or understanding and peace (and whether he was betrayed by his minion Milhouse and ripped apart by snowmobiles until he died). One side cries Bart's catchphrase "Eat my shorts", the other cries "Cowabunga" and both sides engage in a bloody battle.
IGN called this episode the best episode of the sixteenth season. They thought of it as a great episode that dealt with the sensitive topic of religious tolerance, stating that "with a daring story, we can't help but remember when The Simpsons was an edgy hip show that would frequently shed a light on cultural complexes". They thought it would be ideal if there were more episodes like this one.