The new school year has begun for Trinity, a Catholic high school. Jerry Renault, a freshman, is being pulverized during football tryouts. The coach, however, is impressed by Jerry's ability to take a beating and come back for more. He tells Jerry to come back the next day.
Obie, the secretary of a secret gang called The Vigils, is sitting in the bleachers talking with Archie, one of the leaders. Obie is tired of Archie's demands as a leader of the gang, but unable to think of a way to best him. Archie is listing off the boys that he will ask to do special Vigil tasks this year. One of them is Robert Goubert, known as "The Goober" because of the awkward way he runs. Another is Jerry Renault. Obie argues that The Vigils should leave Jerry alone as his mother recently died. Archie insists that Jerry be given the chocolate assignment.
Archie is called in to talk to Brother Leon, a teacher at the school with a sadistic streak. All the students are wary of him, as they never know when he will call a boy up to the front of the class and subject him to some kind of humiliation. Brother Leon tells Archie that this year's chocolate sale is extremely important. Each boy must now sell 50 boxes of chocolate if the school is going to recoup the money Brother Leon's already invested in the project. Brother Leon asks Archie for his help. Archie plays dumb, asking what one boy can do to help the sale. Brother Leon insists that Archie knows how he can help. Archie tells him that The Vigils will get behind the chocolate sale.
The Goober is called before The Vigils and given his assignment. He must sneak into Brother Eugene's classroom at night and unscrew all the desks and chairs until they are barely held together. Then, when the students arrive the following day to sit on them, they will fall apart. Carter, the president of the gang, hands a black box to Archie. It is standard Vigil practice that the one who makes up the assignments, in this case Archie, must face the possibility of doing the task himself. Inside the box are five white marbles and one black. If the black marble is drawn, Archie must do the assignment. In three years, he's never lost the draw, and today is no exception.
The Goober sneaks back into Brother Eugene's class after hours to begin his task. Although he feels bad, he's too afraid to betray The Vigils. He thinks about how much he loves to run as he unscrews the furniture. He's there for six hours before two masked boys sneak in to help him. It takes another three hours to finish the job.
At home, Jerry remembers his mother, her long illness and her death. His father, a pharmacist, often works nights. Jerry wonders whether this is all there is to life: working hard and watching your wife die. He asks his father if he ever wanted to do something more, like go to medical school. His father tells him no, but Jerry's unsure whether he believes him. That night, he stares at himself in the mirror and sees his father's face. Jerry determines to do more with his life than his father.
The Goober has done his assignment well, and the following morning all the desks in Brother Eugene's room collapse. Archie hears the commotion and stops to enjoy the chaos The Vigils have caused. Brother Leon overhears someone giving the gang credit, and he pushes Archie up against the wall. Brother Leon accuses Archie of having something to do with the destruction, but the boy denies it. Archie is angry with Brother Leon for trying to humiliate him in the hallway, but he soon recovers when he sees Brother Eugene crying in his room. Jerry does well at football practice that afternoon, but his success is tempered by the discovery of a note from The Vigils with an assignment.
The following day, as Brother Leon calls the roll for his class and asks each boy if they will accept their 50 boxes of chocolate to sell, The Goober sits in agitated silence. He feels guilty over his part in the destruction of Brother Eugene's room, even though it's already been put back together. His mood is darkened further when Brother Leon calls Jerry Renault's name, and Jerry doesn't respond. When forced to reply, Jerry tells the teacher that he doesn't want to participate in the chocolate sale. Brother Leon is angered at Jerry's actions, and The Goober is afraid for his friend. As the week continues, we see several boys' attempts to sell their allotted chocolates, but every day Jerry refuses to participate in the sale.
Brother Leon lectures a straight-A student who has come in asking how he could have failed the latest test. Brother Leon tells him that pass/fail tests are tricky. A teacher may be looking for something very particular in an answer, and if it isn't there, the student fails. Leon then brings up Jerry Renault and what a troubled kid he must be. The student tells Brother Leon that Jerry was forced by The Vigils to refuse to sell the chocolates for 10 days. Brother Leon checks his calendar and realizes the assignment will be up on the following day. He tells the student that he will review the student's test at the end of the semester to see if he might change his mind about the exam question.
The following day, when Brother Leon calls his name, Jerry still answers "no" to selling chocolates. In his bed that night, Jerry doesn't even know why he did it. He had looked forward to the end of the assignment, of getting his life back to normal, but something about the hatred in Brother Leon's eyes had caused him to refuse the chocolates once again. The next morning, Jerry feels hung over after a restless night. He thinks he'll accept the chocolates today, but other students congratulate him for his defiance. Despite his regrets, Jerry again refuses to sell the candy.
As Jerry's protest continues, other students talk about refusing to sell chocolates as well. Obie has a conference with Archie, in which he warns that Jerry's refusal to participate in the sale not only angers Brother Leon, but also is an act of defiance to The Vigils. Jerry's assignment had been to start selling after 10 days. Now that he's in his third week, other students are wondering if The Vigils have lost their influence.
Sales of chocolate plummet, and Brother Leon is furious. He calls Archie on the phone and demands the boy use The Vigils to help the sale. Archie isn't intimidated as he's learned Brother Leon has used inappropriate funds to buy the cases of candy and will be in trouble if the money isn't recouped. Brother Leon threatens to abolish The Vigils if they don't help the sale.
Before Archie can inform the teacher what he knows, Brother Leon hangs up the phone. The Goober tells Jerry that he is quitting the football and track teams at Trinity. The guilt he feels over the destruction of Brother Eugene's room is overwhelming. The teacher was put on sick leave. The Goober says there is something evil at the school that goes beyond The Vigils. It permeates the school and he won't have anything to do with it anymore.
The Vigils call Jerry in for "a talk" to try and convince him to sell the chocolates, but Jerry again refuses. The gang then tries to enlist another student's help, but he refuses also. Carter beats the boy, tired of The Vigils being defied. Archie argues that they can't beat up every student in the school, but he has a way to turn the tide. The Vigils will make selling the chocolates a matter of school pride. They'll make it cool. By the end of the week, boys will be vying for the chance to sell more candy, and Jerry will be ostracized. Carter informs Archie that they'll adopt this new plan, but Archie is on probation until the outcome.
Jerry's life becomes an endless cycle of abuse. Someone breaks into his locker and destroys an inspirational poster and his new gym shoes. At football practice, he is illegally and violently thrown to the ground. At home, he begins to receive prank calls at all hours of the day and night.
The Vigils begin threatening other students to get behind the sale. They also use their influence and cars to sell boxes of candy to different areas of town. The sales numbers begin to climb. The Vigils attribute their sales to other students so that everyone looks good and receives praise but Jerry.
Another student demands to know why Jerry isn't selling any candy. Their animosity toward him grows as Jerry says that the sale is voluntary and he doesn't want to participate. The Goober is ashamed and angry when The Vigils give him credit for selling his 50 boxes of chocolate when he knows he's only sold 27.
Archie has bribed another boy, Emile Janza, to bully Jerry. Archie claims to have taken a picture of Emile masturbating in the boy's bathroom and will reveal it if Emile doesn't do as The Vigils ask. Emile doesn't mind doing the bullying, but would rather not have the picture made public. He tries to bait Jerry into a fight on the way home, but Jerry ignores him until Emile claims he's homosexual.
When Jerry argues back, Emile calls for a group of boys from the town to attack him. Jerry returns home severely beaten. He hides in his room so his father won't see him. That night, boys taunt him from the street. Others call the house, waking his father. Jerry feels guilty for causing his father to lose sleep but doesn't admit to what's been going.
Archie sets up a boxing contest between Jerry and Emile. Jerry agrees to it as a way to get revenge on Emile for his attack. Emile does it for the pleasure of hurting another person. Archie holds back one box of chocolates, presumably Jerry's, to raffle off at the match. Spectators can also buy tickets to "call" the match. Each ticket allows the buyer to put down which boy they want to throw what kind of punch. The opponent cannot block the punch. The match will not be a free-for-all, but will be dictated by what is written on the tickets drawn until one opponent is down.
Archie has read the school correctly: The students are greedy and cruel. They want to see someone beaten to a pulp, and they want the chance to win the chocolates. To Archie's surprise, Obie calls for the Black Box before the match. He hopes that Archie might finally draw out a black marble but he doesn't. The match begins.
All goes as planned until someone's ticket calls for Emile to punch Jerry in the groin. Archie realizes he never said the groin was off limits, and Jerry instinctively blocks the punch. The crowd is angry, not realizing what happened. They call for Emile to finish off Jerry, which he does.
Although Jerry gets one good punch in, he is beaten unconscious. Some students call for Emile to kill Jerry. Obie spots Brother Leon watching the fight at a distance just before the electricity is turned off. Archie goes to search for the fuse box and is confronted by Brother Jacques who has pulled the power switch. He accuses Archie of organizing the event and nearly getting Jerry killed.
The Goober tries several times to wake Jerry. When he finally does regain consciousness, Jerry tells his friend that he's learned his lesson. A person should just play along with what everyone wants and not try to change the universe. An ambulance is called to take Jerry to the hospital. He has a broken jaw and possible internal injuries.
Brother Leon arrives and tells Brother Jacques that the students were just being boys. Jerry will get the best care, and no one boy is to blame for the near riot. Later, Obie warns Archie that eventually he'll get in trouble for everything he's done. Archie admits that he told Brother Leon about the fight because he knew the teacher would want to watch, and by watching it, the teacher would be sure to protect The Vigils so he himself wouldn't get in trouble. Archie asks if there's any chocolate left, as he's hungry.