The Chocolate War is a story told laconically, in very short scenes and chapters, with brief dialogues and few descriptive passages. We first encounter the main character, Jerry, in the midst of football practice at the all-boys Catholic Trinity High School in the fictional town of Monument, Massachusetts. Jerry wants very much to make the team, perhaps partially because he has recently lost his mother to cancer. Archie, the "Assigner" and brains of a secret organization called The Vigils, watches from the stands. Obie, the secretary of The Vigils, waits with him, taking down notes of Archie's hazing "assignments." The assignments are cruel pranks and practical jokes to be performed by selected students, who have no choice but to obey The Vigils or face the consequences.
Later, Brother Leon, the acting headmaster of Trinity, calls Archie to his office and conspires with him to recruit The Vigils to help with the annual school chocolate sale. Leon is only temporarily in charge of Trinity, because the real headmaster is in the hospital. The power-hungry Leon has overextended school funds to get a bargain on the chocolates, fulfilling Archie's later comment that all people are "greedy and cruel." He wants the students to sell exponentially more boxes than the have in previous years, and at higher prices. Archie agrees to help Leon with the chocolate sale.
Archie assigns various tasks to students, including Jerry's best friend, Goober. Goober must unscrew every single screw on every single piece of furniture in a classroom (a task that would have been impossible had certain masked Vigils not shown up in the middle of the night to lend a hand), causing a raucous collapse during school the next day. The disruption so upsets the teacher, Brother Eugene, that he must go on a leave of absence. The incident fills Goober with guilt, and he begins to become disenchanted with Trinity.
Jerry's assignment is to not participate in the chocolate sale for ten days, thereby openly defying Brother Leon. He completes the ten-day run, but, having been affected by the ugly culture of deceit and cruelty around him, decides to defy both Trinity and The Vigils by continuing to refuse to sell the chocolates. This leads to heavy persecution of Jerry by The Vigils: they vandalize his property, beat him severely, and arrange for his ostracism by the community at large.
Both Archie and Leon are threatened by Jerry's defiance, feeling that they will both be destroyed if the chocolate sale fails. Archie manages to rally The Vigils into making the sale their personal project, organizing teams to sell the chocolates and make it a success. Brother Leon knows that Archie is the one responsible for this, and he allows the violence against Jerry to continue. Jerry's final punishment comes when Archie organizes a cruel gladiatorial boxing match in front of the whole school between Jerry and a bully named Emile Janza.
The fight is scripted by the spectators, who purchase tickets on which to write descriptions of the blows they want to see. The blow that wins the fight will be the winning ticket of the raffle. Janza and Jerry fight, and Jerry is outmatched by Emile's size and strength. Even though Jerry gets in some good hits, Janza stops playing by the rules and pummels Jerry mercilessly. Jerry is beaten so severely that he loses consciousness. His jaw broken, he is taken by ambulance to the hospital. Before he leaves he tells his best friend to go along with whatever Trinity and The Vigils want him to do in the future, or he may end up like him.
The main theme of this novel is defiance of authority. The story is told in extremely simple language, without slang or regional affect to taint the descriptions of typical adolescent interactions. There are no female characters, and the story is about the boys and the school, rather than their families or lives outside of Trinity. It is a raw, emotional book, full of realistic and sometimes graphic detail.