The episode begins with the Marsh family leaving for church. Stan, in a cast from being shot in the previous episode, is annoyed about having to go every Sunday. Sharon and Randy discuss about how much better they feel when they go to church.
The family arrive, along with the other townspeople. They all act friendly to each other, with Randy holding the door and even feeling pity for a woman who's missing the sermon. Inside, Father Maxi begins his sermon, speaking about what God has to give us. He is interrupted many times by the adults heckling him with Catholic priest jokes and laughing at each other. Maxi tries to calm them, but fails.
The adults all leave at the end, laughing at all the jokes being told. In the Marsh car, Stan questions the point in the jokes, describing it as "stupid". Randy berates him, saying comments like that will make him go to hell. Back at the church, Butters comes to visit the upset priest. He explains that he knows how it feels to be bullied, and explains Maxi needs to just put himself out there.
At game night at the Marsh house, the boys are playing Western Legends. Butters comes in, bringing Maxi with him to play. The gang, confused, start playing, but are disturbed by his Bible quotes. Butters attempts to make Maxi look good by mentioning his singing hobby, but they are spotted by Randy, who starts ridiculing Maxi. Maxi then leaves, with Butters coming after him, leaving Cartman to question who invited Butters to game night. Outside, Butters catches up to Maxi and tries to make him feel better about himself. He tells Maxi that if people want to hurt him, "fuck 'em".
The next Sunday, the townspeople arrive at church, once again being positive and friendly, but when Randy tries to open the door, he finds it locked, leaving the townpeople to worry. Butters comes out the church and is subjected to ridicule. He tells everyone there is no church and slams the door. Back in the Marsh car, the parents are upset about not being able to ridicule the priest. Shelly questions why this is a big deal, and is yelled at by Randy.
Maxi and Butters are sitting round a campfire toasting marshmallows. The two are happy and become friends. A montage is shown of the two doing various activities together, while Faith In Christ plays. These activities vary from walking and rowing, to watching movies and playing. Some of these activities are seen by the townspeople, who look on confused.
At the cathedral in Denver, the archbishop gets a call from Mr. Mackey, who informs him that the priest has gone missing. The archbishop believes he means the priest has run off with some boys, and calls the Catholic Cleanup Crew to sort him out.
At Kidzone Roller Rink, Clyde is having a party to celebrate his birthday. Butters comes in, bringing Maxi with him. Clyde is angry, as he doesn't want a priest at his party. Butters guides Maxi through how to skate, as the other party-goers watch on, confused.
In Skeeter's Bar and Cocktails, the townspeople are drinking, depressed about not having church. Randy and Stuart discuss how meaningless life is, before someone runs in to exclaim that there are people in the church. The townspeople run into the church, only to find the Catholic Cleanup Crew there. They inform the town that nothing weird has happened and Maxi has just gone to South America. Randy tells them that he was in his house the other day, but they deny it. The town walk out, sad that they cannot go back to church yet.
At the Marsh house, the clean-up crew start bleaching the kitchen table, only to be spotted by Stan. Stan, like his father, tells them that Maxi was there the other day. One of the priests then wipes Stan down with a "Kumby".
Back at the roller rink, Clyde is blowing out his candles, much to the joy of the boys. Maxi then starts repeating bible verses again. Aggravated, Clyde and Cartman tell Kyle to sort it out. Kyle takes Butters into another room, where he explains no-one wants Maxi there. Maxi overhears and leaves, depressed. Butters, angry, also leaves. The clean up crew then turns up to clean the rink. Clyde, angry, yells at them, threatening to tell the police.
Butters wanders through a parking lot looking for Maxi. He finds him by a dumpster. Maxi berates him for not leaving him alone, telling him he hates himself because he couldn't stop the priests from molesting children. He then tells Butters to go away. Butters walks down the streets, lonely. The Catholic Cleanup Crew drive up to him and try to entice him into getting in their van, eventually succeeding by telling him about the bunny in the back. Butters finds Stan and Clyde in the van, and the three are locked in.
At the Marsh house, Randy is bored flicking through the TV channels. Maxi comes round looking for Butters. Randy tries to get him to come back, and tells him about the clean up crew, leading Maxi to worry. In the car, Randy calls up Stephen, explaining the boys have been kidnapped by priests. The two, along with Linda, crack some jokes, leading Maxi to angrily snatch the phone and question if Butters has told him anything. Stephen tells him about a message saying he had to do some camping, leading Maxi to realize where they are.
At the campsite, the 3 boys are tied up, with the cleanup crew trying to trap Maxi. They have a bigger machine, known as a Kumboni, to deal with him. Maxi eventually turns up, expecting to be killed. They tell him he's actually being transferred, which Maxi seemingly accepts and leaves. The priests begin to celebrate, before Maxi turns up again on the Kumboni. Driving it, he runs over and kills all three of the clean up crew and rescues the 3 boys. He explains to them that he has realized his purpose, to protect all the boys.
Maxi reopens the church to the happy townspeople. He gives a sermon about penance, which is once again interrupted by the Catholic priest jokes, but, after what he has been through, he learns to accept them, and not be disturbed by them.
AV Club gave "A Boy And a Priest" a "B+" rating saying: "This episode isn’t an all-time classic like “Red Hot Catholic Love,” but much like last week’s episode, it handled a dark, difficult topic with the appropriate mix of irreverence and empathy. Trey and Matt are clearly embracing their role as social commentators, and so far, the results have been thoroughly rewarding."
IGN gave "A Boy And a Priest" a "8.2" rating saying: "This week's South Park offered a better sense of how the new season will set itself apart. The idea of looking back a decade or more to revisit classic South Park episodes is definitely appealing, and hopefully this won't be the last time we see that approach in Season 22. This episode managed to mine more comedy and drama out of a familiar conflict, showing just how little the world has really changed during South Park's long, long run."