Meet Jerry Renault, the hero of The Chocolate War. We find him on the football field, taking a beating. Not a literal one, just normal football practice abuse. He's a freshman at Trinity High School, and wants to make quarterback. His friend, The Goober, has already warned him to show no fear. The coach wants to see how much he can handle. After practice, Jerry muses about the recent death of his mother.
Now we meet some villains, Archie Costello and Obie, members of Trinity's secret society, The Vigils. Archie (the mastermind) and Obie (one of his thugs) are in the bleachers, picking their newest victims. They decide that Roland Goubert, The Goober, will be given an "assignment" (2.16) having to do with Brother Eugene's classroom. Jerry, Archie decides, will get an assignment that has to do with chocolates. Obie protests, saying that Jerry's mom died only last spring; they should leave him alone. But, Archie isn't swayed.
Soon, Archie learns that Brother Leon, the sadistic teacher, has ordered twice as many chocolates as last year, and he wants Archie and the Vigils to make sure they get sold as part of the school fundraiser. Archie is a bit reluctant, but agrees to help him make the sale a success. Next, The Goober is getting his assignment from The Vigils. He has to go to Room Nineteen, Brother Eugene's classroom, and unscrew all the screws in all the furniture, so that when you touch it, everything falls apart.
We cut to Jerry, who is in Brother Leon's homeroom. Leon is tormenting a kid named Gregory Bailey and we're starting to see how twisted Leon really is. After a brief introduction to Emile Janza, another bully, we find The Goober in Room Nineteen, trying to do his assignment. When he's on the verge of giving up, some masked Vigils come in and help him finish the job.
Then, we get a glimpse into Jerry's home life. His dad is a nice guy, but Jerry's thinks he's stuck in a boring routine. Jerry doesn't want to turn out like that; he wants something more, though he isn't sure what.
Now we're in Brother Eugene's classroom, watching all of the screw-less furniture fall to pieces. Archie is standing by the door, very pleased with himself for thinking this prank up. When Brother Eugene starts crying, he's even more pleased. Then, after football practice, Jerry finds a note on his locker, summoning him to The Vigils' secret hideout, a supply closet behind the gym. The Goober is really bummed since the Room Nineteen prank. He feels awful that it made Brother Eugene cry. He's also afraid his involvement will be discovered and that he'll be punished.
Today is the first day of the chocolate sale, and Brother Leon is using roll call to get kids to commit to selling. When he gets to Jerry, Jerry flat-out refuses the chocolates. The Goober can't believe it.
Later we meet up with Archie and Emile. Emile thinks Archie has a picture of him masturbating in the bathroom at school. But, Archie didn't even have any film in the camera when he pretended to take the picture. Now he's using the fake picture to blackmail Emile. Emile, who also wants to be a Vigil, tells Archie he'll do anything to get the picture back.
Now we're back to Brother Leon and the chocolate sale. We find out that Jerry has been refusing to sell the chocolates because The Vigils made him. That was his "assignment." Tomorrow, however, Jerry is supposed to accept the chocolates just like everybody else. But, he doesn't. He says "No" again. He wasn't planning on refusing to sell the chocolates, and isn't sure why he says "No," though he knows it has something to do with standing up to Leon and The Vigils.
Obie convinces Archie that they need to force Jerry to sell the chocolates. By continuing to refuse the chocolates, Jerry is undermining The Vigils' power. Soon, the other students won't respect them. Plus, Archie promised Brother Leon that The Vigils would help with the sale. The Vigils don't want to be on Leon's bad side.
Next, we see Leon grumbling about the low chocolate sales. He totally blames Jerry, and wants to see something done about him. So, he gets Archie on the phone and tells him to make Jerry sell, and to do whatever it takes to get the chocolates sold. If not, Leon will destroy Archie and The Vigils.
So, the terrorization of Jerry Renault begins. The guys on the football field seem like they want to actually kill him. A giggling anonymous caller is ringing his phone off the hook. Somebody trashes his locker. Meanwhile, Archie and The Vigils are able to make selling chocolates seem cool, and Trinity is in a chocolate-selling frenzy.
Lots of students are mad at Jerry for not doing his part to make the sale a success. Things take a turn for the worse when Emile Janza and at least ten other guys brutally attack Jerry in the pathway between the football field and the school. Jerry wants to tell his dad, but is afraid his dad will get hurt, so he doesn't.
Finally, all the chocolates have been sold – except for the fifty boxes Jerry was supposed to sell. Archie begins planning some kind of raffle of these chocolates. He calls Jerry and offers him a chance to get revenge on Emile Janza. Jerry accepts, and he and Emile both show up to the athletic field at night. They are led to the platform and told the rules of the game. Basically, Carter will draw a raffle ticket and read what the owner has written. Students have written in the name of the person they want to get hit, and how they want that person to get hit.
Jerry and Emile both get in a few punches, but then everything goes out of control. Emile's taking it too far, and though Jerry manages to fight back some, he's no match. Plus, the students are all screaming for his death. The Goober shows up near the end of the spectacle and calls for the fight to be stopped, but nobody hears him.
The fight ends when the lights on the field go out. The students run off, and Archie heads to the utility room to see what happened. Brother Jacques is inside with his hand on the switch. He starts to lecture Archie, but soon Brother Leon comes to Archie's defense. Meanwhile, The Goober is with Archie and they are waiting for an ambulance. Jerry wishes he could tell his friend not to defy authority, because it's too dangerous. But he can't talk.
The novel ends with Archie and Obie walking home together in the dark.