It is the spring of 1965 in a middle-class section of Brooklyn, New York. St. Basil's Catholic School For Boys is having mass and a liturgy is being performed, then music. A mischievous younger kid has a clicker with him that's used as an indicator to stand or sit down and disrupts the music service with the kids sitting up and down. He is caught by Brother William and taken away. Sixteen year old Michael Dunn, an unassuming and sensitive quiet kid, is new to the school transferring from Boston from St. Mary's Catholic School, his parents apparently having died in an accident.
He is interviewed by the soft-spoken and compassionate, but strict Brother Thaddeus, the headmaster of the school. Dunn is nervous, doesn't know the "right" answers to questions addressed to him, unintentionally interrupts, and keeps forgetting to say "yes Brother Thaddeus" to every question asked and comes out of the interview emotionally drained. In English class, it is led by brother Constance, a prim, bespectacled, forthright, and very strict teacher He gave the kids an assignment on the Holy Trinity and catches Rooney, one of the boys talking without permission. Since Rooney decided to talk without permission, he is instructed to explain the homework assignment and makes up the Holy Trinity as being total mystery, making it evident he didn't do his homework. Brother Constance notices he did not do his homework assignment, takes the boys head, and slams it against the blackboard insisting he apologize. Then he's forced to eat the paper in front of the class.
Dunn's fellow classmate Caesar, who wanted to give the definition to the class, but was caught with gum in his mouth and made to stick it on his nose, turns around and tells Dunn "Welcome to St. Basil's", in an ironic way. Brother Constance is clearly a hothead and control freak with some serious issues that wants the students under his complete submission and will embarrass or strike them with any little infraction. Dunn and Caesar have lunch together.
Caesar is an overweight, bespectacled, and snooty intellectual that has aspirations to go to Harvard to be a psychiatrist. Rooney frequently teases Caesar about "being a faggot", whereas Caesar thinks Rooney is a moron and prima donna. Caesar prides himself that he's never been assaulted by the faculty and wants to stay clean so he can get into Harvard to become a psychiatrist. Back at Dunn's grandparents, they are having a traditional American Irish dinner of corned beef, cabbage, and potatoes. His chain-smoking, opinionated, and controlling grandmother is commenting on the Italian pope coming to America and seems to have a disdain for Italians. And she already has plans for Michael to be a priest, or better yet bishop or pope to please her and his deceased parents. Dunn's younger sister has a tic for gathering and playing with the flowers in a vase on the table.
They both practice his Latin lesson together. Rooney and his gang are walking to school together and he's hitting on Jeanine from the girls Catholic school. Rooney is an uncouth and not very bright student at the school that wants to be the alpha male with his buddies Corbett and Williams. Rooney sees Dunn and Caesar and teases Dunn, seeing this as an opportunity to make himself look good, knocking his books out of his arm trying to test him.
Dunn brushes him off and tries to pick up his books, but Rooney grabs him. A tomboyish teen girl, Danni, that runs the local soda fountain, comes over and tries to put a stop to it. Caesar tells him he'll give him a banana or doggie biscuits if he stops. Rooney lets Dunn go, but tells him if he keeps hanging around Caesar, he (Dunn) will start thinking he's cute. Dunn and Caesar are using the restroom with Caesar assuring Dunn he will get him caught up on his homework.
Caesar insists Rooney calling him a "faggot" is just projecting his doubts about his own sexuality. And there is no toilet paper for Caesar. He says he'll come up with something with his homework assignment in his handBack in the classroom, Rooney is removing the screws from Caesar's desk chair as a prank. Dunn catches him doing it the second he walks in the room, but dismisses it. Then Brother Constance enters with Brother Timothy, new to the school and the order, as an observer. Caesar enters the class late and given a demerit.
Then he does not have his "misplaced" homework assignment and given an additional one. Caesar sits down and his desk falls apart with him falling on the floor. Brother Constance realizes it's a prank and makes all the boys get on their knees until the perpetrator comes forward. He catches Dunn whispering to tell Caesar he wanted to warn him.
Dunn is told to come forward because he knows about it. Refusing to rat out Rooney and afraid of repercussions, Brother Constance slaps Dunn in the face and hits his palms several times with a paddle ironically marked with the word "patience". Refusing to answer Brother Constance, Dunn is thrown towards the class to point out the perpetrator. Rooney smirks at Dunn and Dunn jumps at him, with them broken up.
Dunn and Rooney are in Brother Thaddeus' office on their knees and forced to hold two heavy books. Brother Timothy asks to talk to Thaddeus in private. They both stroll in the courtyard with Timothy explaining how sadistic and brutal brother Constance is and that it was a bad example of how a classroom should be run, but Thaddeus insists Timothy has a lot to learn being a newcomer to the order and that Constance is a very good and effective teacher and not to be quick to judge him. Rooney and Dunn are leaving school. Dunn wants nothing to do with him, but Rooney wants a friendship because he now feels his ego has been bruised and needs to save face. Dunn reluctantly agrees and they go to the local soda fountain in the neighborhood, a place St.
Basil's has set off limits for the boys, but many attend anyway. The soda fountain is run by Danni, the girl trying to break up Dunn and Rooney earlier, that is not attending school, but caring for her near catatonic single father. Rooney tries to be friendly with Danni, but she refuses his advances. Rooney tells Dunn not to waste his time with her. Brother Timothy comes in the soda fountain, much to the shock of the kids, but purchases a pack of Chesterfield cigarettes. Then two of the brothers from the school invade the place and the kids try to escape and not get caught. One of the brother's is extremely surprised to see Timothy there.
Dunn helps Danni clean up the mess and right away she sees he's a good person and friend she can talk to. The boys are all naked standing next to the pool in physical education with the Singing Nun's Dominique playing on the radio, but the brother in the office reading a newspaper is annoyed by it and immediately switches it to Franz Shubert's Marche Militaire playing on the radio. Their instructor, Brother Paul, tells them they are out of shape and need to shape up like men with a possible invasion by the Communists with the escalating Vietnam War, who want to kill Catholics. Caesar keeps blowing his nose making noise annoying Brother Paul, who threatens to punch him if he doesn't stop. Dunn and Caesar are in the library studying. Rooney approaches Caesar that because he was found to have called Constance a "Goddamn faggot" during their kneeling and that he's being removed from the varsity team unless he goes to apologize to Constance. Fearing physical punishment or other discipline, he realizes his grades are all he has to depend on, which are very bad. He wants Caesar to work with him, but Caesar totally refuses, despite his pleas.
It is confession time and Rooney is taking the lists of his friends confessions and changing them to lesser offenses so they will be in less trouble. Dunn is confessing to a priest that keeps egging him on about his reading of a pornographic magazine. And Kevin, the kid who pulled the clicker stunt during mass, is pulled out of the confessional and called a weasel by Father Abruzzi. Rooney sneaks into the confessional pretending to be Caesar's confession hearing priest.
Caesar confesses he plagiarized an essay article to win a prize and doesn't want to lose his chance of going to Harvard University. Rooney reveals himself that now he has that on him and that Caesar WILL help him get passing grades and to forget Harvard otherwise. A dance is being held at the school for the boys and visiting Virgin Martyr girls. Brother Timothy is presiding and introduces Father Abruzzi, who tells the kids that the dances are to teach the kids how to interact with one another, but then goes into hysteria warning the kids about the evils of lust and that they could burn in hell forever if they give in to it. But nevertheless wishes them a good time for the night. With nearly all the other kids dancing, Dunn, Caesar, and Jeanine's friend Cathleen are not dancing. Dunn walks over to the soda fountain to see Danni and visits with her. They converse for a little while and Danni reveals to Dunn that her father divorced her mother and the woman her father was messing with killed herself and he's been in a state of melancholia every since.
Rooney finds Caesar in the men's room and offers to take Caesar in a ride with Cathleen with them in his father's brand new Lincoln Town Car. Caesar begrudgingly accepts his invitation simply to avoid anything being told about his earlier confession. Rooney takes his father's brand new Lincoln out of the garage, despite not having a license with Jeanine, Caesar, and Cathleen in tow. Caesar and Cathleen remain in the car parked on a bridge. Rooney and Jeanine are making out and getting drunk on Jack Daniels. Cathleen reveals to Caesar she loves his intellect and the article in the newspaper.
The assumingly asexual Caesar gladly receives Cathleen's advances and makes out with her. Meanwhile Rooney and Jeanine are as well, but she throws up on him just as he is about to make love to her. A boat is about to cross and the bridge needs to be raised. Rooney barely makes it back into the car in time and the axle falls out of the car into the water with the car partially destroyed. The boys and girls from both schools are at 5th Avenue in Manhattan waiting for the Pope's arrival.
Rooney's face is bruised from his father who just returned home after what happened to his car and tries to hit on Jeanine and convince her that if the pope sees them and blesses them, they can have sex without sin, but she dismisses him and an angry nun grabs Rooney and takes him away. Just as the Pope is passing through, "The Barber of Seville" is playing on the soundtrack in a parody of the Italian culture and pope and the boys sneak out past the brothers. In a hypocritical moment of reverence, the brothers cross themselves with the Pope's passing and Brother Thaddeus is moved to tears. Brother Constance is frustrated at the boys missing while taking attendance for the bus. Rooney, Dunn, Caesar, Corbett, and Williams are all in a movie theater watching Elvis Presley in "Blue Hawaii" assuming they won't be caught.
Rooney is making crass comments on Elvis remaining a gentleman and singing while surrounded by beautiful Hawaiian girls while singing "Hawaiian Wedding Song". The five boys are reprimanded by Brother Constance that he will "make their miserable lives more miserable than ever before Easter" and have them cleaning the statue in the school's courtyard every Sunday. They are cleaning the statue with toothbrushes with birds constantly flying around and leaving droppings on it. Brother Thaddeus looks on out his office window with a smile on his face apparently showing how much he cares for the boys. Dunn and Brother Timothy hang out in the courtyard and converse after having been in an empty church meditating. Timothy is more friendly and laid-back than the other brothers and one you can talk to and be yourself. He tells Dunn that he was written off as the bum of the family, but joined the order nevertheless.
Danni has lunch at Dunn's house. His grandfather seems pleased to have her over and attempts conversation with her, but his grandmother isn't pleased because she doesn't want him to be with a girl and concentrate on being a priest. Williams, the chronic sex fiend, is taking part of a ceremony with dozens of girls taking communion wafers with him assisting a priest. All the girls opening their mouths to receive the wafers is overexciting him and he passes out. Dunn and Danni are on a date at Coney Island at a food stand and she teaches him to dance to Otis Reading's "I've Been Loving You Too Long". They hang out at the beach, embrace passionately under the boardwalk and make out. Dunn has returned home with his grandmother asleep at the dinner table with a cigarette still burning. Dunn and his sister Boo converse with her afraid Dunn will leave her because he loves Danni.
He assures her he will never do so. Back at the soda fountain after school, Rooney and Caesar are working on the David Copperfield book report. Caesar is helping him edit it, much to his frustration of being at the soda fountain. Two brothers are about to invade the place again to report the kids, but this time, Danni stands up to them, locks the door, and draws the shades. The two brothers leave.
During the lavish evening meal with all the brothers and the headmaster, Brother Paul tells Brother Constance about the situation at the soda fountain, with Constance declaring the girl as a delinquent and that she needs to be arrested and the place shut down. Brother Timothy disagrees and Brother Thaddeus is annoyed at Constance's judgmental attitude of the girl, stops the arguing, and that he wants to enjoy his dinner. Back in English class, brother Constance is handing back the graded book reports on David Copperfield to the five boys on their knees. Rooney is delighted to have received a good grade, but Caesar is disappointed at the A minus because he declared Charles Dickens as a paranoid schizophrenic. The boys are walking home from school and the police have ordered Danni to have her shop closed down, with she and her father being escorted out by the police and social services, with the brothers having ordered this. Dunn and Danni embrace and tearfully farewell, thinking they will never see each other again.
Late at night, the other four boys break into the school courtyard with Rooney declaring they are doing it for Dunn. They decapitate the statue they have been cleaning the last 2 Sunday's. Brother Thaddeus is preaching to the boys in an assembly in the school auditorium and while he's doing so, Rooney shows Dunn the decapitated head in a duffle bag. A very angry Brother Constance storms into the room calling out the five boys to come with him, with Brother Thaddeus concerned and having his speech to the assembly temporarily stammered. They are escorted down the hall by Constance and locked into a closet temporarily. Rooney is worried that they've now been caught and Caesar sneers at his comment about the brother's knowledge. Rooney tries to figure a way for them to talk their way out of it and Caesar tells him he will try to reason with Constance, but Rooney dismisses the idea of "reasoning with a grown man in a dress".
Brother Constance has the boys brought out to him and lined up in the school gymnasium by Brother William. He primly and sternly tells the boys he refuses to hear any of them deny they're guilty and is convinced at least one of, if not all of the boys are the vandals and asking the guilty party to admit it. Dunn admits it, even though he didn't. It turns into an argument, but Constance puts a stop to it and has Corbett bend over an exercise horse and gives him five lashes with a leather strap, Williams six lashes, then Caesar, who is the next in line declares he is exempt from corporal punishment from a laminated doctors note from his uncle stating he's subject to seizures.
Brother Constance refuses to comply with the doctor's note and listen to Caesar pleading for another punitive plan and grabs Caesar whipping him endlessly. In a fit of rage, Dunn pushes Constance to the floor telling him to leave Caesar alone. He runs back into the auditorium while Brother Thaddeus is still giving a speech with a puzzled crowd seeing him scared. Constance storms in the door with a concerned Brother Timothy standing up and wanting to put a stop to it. Constance grabs Dunn and he resists and is slapped in the face by Constance, who calls him a "bastard" and "impudent piece of trash".
Then a bruised Dunn gets up and punches Constance in the mouth and most of the school cheers him on. Brother Thaddeus shows no emotion of the incident. The five boys are outside Brother Thaddeus' office with Constance demanding they be suspended and Brother Timothy arguing it was self-defense. Brother Thaddeus brings the boys inside and tells them they are all guilty and will be suspended for 2 weeks. Dunn declares he is responsible, but Thaddeus tells them they all acted as one, but that Brother Constance started it. Brother Thaddeus, apparently having a change of heart after hearing Timothy's testimony a few weeks ago and from what he's witnessed in the assembly hall, gives Constance a letter of dismissal requesting he be transferred out of the school and to never work with children again. Constance is outraged and declares he will take it to the bishop, but Thaddeus dismisses his threats and to take them out of his office.
Brother Thaddeus requests Brother Timothy to replace Constance, which he accepts. At the end, the boys are worried at the fact they are suspended, but are delighted that they won't have to be at the school for 2 weeks. During the credits with Elvis Presley's "Blue Suede Shoes" playing, Rooney narrates that in 1966 the boys all graduated from St. Basil's except for him. Caesar graduated from Queen's College with honors to become a psychiatrist (his inability to perfectly navigate the minefield of St. Basil's prevented him from attending Harvard), Williams got a job as a projectionist at the Peekaboo Theater in Time's Square (a dream job for his problem with chronic masturbation), Corbett married Jeanine and had five kids (stuck to the old Catholic ways), Dunn and Danni bumped into each other at Woodstock (apparently Dunn became a hippie disillusioned at the hypocrisy of organized religion and Danni probably spent her late teen years in foster care after the soda fountain was closed down), and he (Rooney) got a job as a shampoo boy at a beauty shop in Bensonhurst after having failed to graduate high school and beautician school and surrounded by "funny guys" (apparently Rooney never having come to terms with his true sexuality and failed attempts with girls).