In 1965, Boston teenager Michael Dunn (Andrew McCarthy) and his young sister Boo (Jennifer Dundas) have been sent to Brooklyn to live with their Irish-Catholic grandparents (Kate Reid &amp; Richard Hamilton) following the deaths of their parents. He is enrolled at St. Basil's, the strict all-boys Roman Catholic school run by St. Basil's church, where his grandmother is determined to see him fulfill his parents' dream of him joining the priesthood after graduation. Dunn befriends Caesar (Malcolm Danare), an over-weight, bespectacled bookworm. Caesar helps Dunn catch up with the rest of the class, but because of their association, foul-mouthed class bully and underachiever Ed Rooney (Kevin Dillon) bullies Dunn with a prank outside of the soda fountain across the street from school.
Not long after this, Dunn enters the classroom at the beginning of his English-Lit class and sees Rooney remove the screws from Caesar's desk. Minutes later, Caesar arrives, sits on the desk and falls to the floor. The teacher, Brother Constance (Jay Patterson) orders all the boys on their knees until one of the students confesses. Dunn then whispers to Caesar that he tried to warn him, but his whisper is caught by Constance. Convinced that Dunn knows the perpetrator, he tries to get the prankster's name out of him by striking Dunn's open palms with a wooden paddle. Fed up with Dunn's refusal to rat out Rooney, Constance shoves him to the floor and orders him to point the guilty party out. Dunn looks up at Rooney from the floor, who delivers a sly grin at him. Dunn lunges towards Rooney, taking him to the floor and the pair are separated by Constance and the novice friar, Brother Timothy (John Heard), who has been observing Constance's classroom teaching and discipline methods that day.
Both are sent to headmaster Brother Thadeus' (Donald Sutherland) office. During a moment alone, Rooney, impressed by Dunn's refusal to snitch on him, attempts to patch things up between them, but Dunn wants nothing to do with him. Rooney tries again after class, but this time tells him that if they don't become friends, then he has to continue in his harassment in order to save face. Reluctantly, Dunn befriends Rooney, along with his friends Williams (Stephen Geoffreys), a sexually frustrated kid who is frequently caught masturbating, and Corbett (Patrick Dempsey), the dull one of the bunch. Dunn also befriends Danni (Mary Stuart Masterson), a teenage tomboy who runs the soda fountain across from the school and takes care of her mentally infirm father (Jimmy Ray Weeks). Looking for mischief by St. Basil's students, Danni's fountain shop is raided numerous times by the Brothers, leaving the shop in shambles. Dunn helps Danni clean things up, sparking a romance between the pair.
At the sacrament of confession, Rooney looks at the lists of sins each of the boys has committed and tells them how to edit them so they don't sound so bad and are yet truthful. When Caesar enters the confessional, Father Abruzzi (Wallace Shawn) becomes preoccupied with another student misbehaving in the church. At that point, Rooney goes into the priest's booth and acts as the priest hearing Caesar's confession, giving him the penance of befriending Rooney and making sure he gets Rooney passing grades. As a result, Caesar joins the four and befriends them while tutoring Rooney.
Later, while the students are attending a St. Basil's school dance, Father Abruzzi gives an outlandish speech to the school along with the girls' school nearby regarding the evils of the flesh and "lust" and how that will condemn them to hell. That night, after getting bored at the dance, Rooney and Janine (Dana Barron), a student at the neighboring Virgin Martyr Girls Academy, drive Caesar and Janine's friend Cathleen (Yeardley Smith) around Brooklyn and get Rooney's father's brand new 1966 Lincoln Continental, getting stuck on the Carroll Street drawbridge over the Gowanus Canal, which destroys the powertrain and most of the undercarriage.
Pope Paul VI visits New York City and St. Basil's school takes a field trip to Manhattan to see him ride in a parade. The five friends sneak off to a nearby movie theatre, where they watch Elvis Presley's Blue Hawaii. After the movie, they are caught missing, and Brother Constance orders them to clean St. Basil's statue with toothbrushes on the school courtyard after Sunday Mass for punishment.
The friendship between Dunn and Danni further develops, culminating in a passionate kiss under the boardwalk on Coney Island in a rainstorm. One day, during one of the Brothers' routine "raids", Danni takes a stand and locks them out. When they look into the windows and try to take names, she closes the blinds. The Brothers leave, but later at dinner, they discuss the episode at the soda fountain. At the urging of Brother Constance and gym teacher Brother Paul, and at the reluctance of Brothers Thaddeus and Timothy, they notify social services. A few days later, Dunn and his friends walk up to the fountain and find police cars and a few of the school's Brothers surrounding the door as Danni's father is led out of the front door in handcuffs. Fearing the worst, Dunn rushes in and finds that social workers are getting ready to take Danni away. A shaken Dunn takes Danni in his arms. Weeping, she wants him to promise he won't be sad over her departure. He watches helplessly as she's taken away in a car.
Rooney, angry at the loss of his hangout and at the Brothers for ruining his friend's life, develops another prank with the help of Caesar, Williams and Corbett. The night before Easter recess, the boys sneak onto the grounds and decapitate the statue of St. Basil. During an assembly the next day, Rooney presents Dunn with a duffel bag containing the missing saint's head. Brother Constance shows up, knowing he's found the vandals, and quietly orders them out of the assembly.
Constance first locks them in a closet, where they discuss possible options. Moments later, they're retrieved by Brother William, who brings the quintet into the gym, where Constance has set up an exercise horse and a wide leather strap. He tells the boys that the guilty can confess now or all will suffer for it. Dunn, though innocent, speaks up. As Constance attempts to lead Dunn up to the horse, Rooney clears Dunn's name, but names Williams, who names Corbett, who names Caesar. Not willing to listen any further, Constance calls Corbett to the horse and delivers five blows from the strap to Corbett's rear. He repeats the same procedure with Williams, delivering six this time. When he comes to Caesar, he is presented with a laminated doctor's note, presumably to exempt him from corporal punishment. Constance says he'll return it to him after he's finished and orders him to the horse. Caesar pleads for mercy, but Constance drags the cowering Caesar on the floor, beating him with the strap while doing so. Unable to watch such brutality any longer, Dunn shoves Constance to the floor, ordering him to leave Caesar alone. Constance gets to his feet, and Dunn flees the gym with the Brother and the other boys behind. The chase ends in the auditorium as Thadeus is concluding his remarks to the student body. Dunn rushes in, knocking over a series of music stands and chairs, followed by Constance, who tries to call him out. He then tries to take Dunn by force, but Dunn resists. Constance backhands him, shouting "Bastard!" as he does. As Constance tries to explain himself before Thadeus, Dunn sees that he's been cut on his cheek from Constance's ring. He jumps to his feet and delivers an uppercut to Constance, knocking him to the floor and causing pandemonium as the student body rises to its feet and cheers for Dunn.
The boys are sent to the headmaster's office, where they are joined by Brothers Thadeus, Timothy and Constance. Constance tries to have all five expelled for assault while Timothy argues self-defense. Thadeus calls the boys in and asks for a reason not to expel them. Dunn, seeing a possible exit from the priesthood through his expulsion, accepts the blame and says he should be expelled. Thadeus counters by saying that since all acted as one, all shall bear the consequences. Dunn protests by saying he instigated the melee. Thadeus disagrees, saying he understands it was Constance who started it. Not explaining anything further in front of the boys, Thadeus suspends all five for two weeks and sends them out of his office. Thadeus hands Constance the signed document, which orders him transferred out of St. Basil's and to where he won't be working with children at all. Angry at what he perceives as betrayal, Constance declares that he will demand an investigation into the matter, taking it to the bishop if necessary. Thadeus, unmoved by Constance's remarks, orders him out of his office. Timothy is then offered Constance's job, which he immediately accepts. The five boys walk out of the school downtrodden after having been suspended, and then joyfully realize they won't have to go to school for the next two weeks.
Rooney is later heard stating that everyone graduated in 1966 "except me." Corbett married Janine and they have six kids, Williams works as a projectionist at a Times Square porno theatre, Caesar graduated with honors from Queens College and went on to become a psychiatrist, Dunn (who presumably didn't become a priest) eventually was reunited with Danni at Woodstock. Rooney went to beauty school "where everybody graduated ... except me," but became a shampoo boy at a Bensonhurst hair salon, where "the hours suck, the pay sucks, and I'm surrounded by 'funny guys,' but the tips are great! Thank you, God!"
What does Brother Constance strike Dunn's open palms with?
Wooden paddle