There is a definite power structure at Trinity high school. Brother Leon and The Vigils use violence and manipulation to control the student body and teachers who might have a problem with their awful tactics. Jerry, The Goober, and some other students try to destroy this power structure by refusing to participate in it. Unfortunately, it's not that easy. The Chocolate War shows just how hard it is for a small group or a single person to stand up to the majority – regardless of who's right and who's wrong.
Jerry is empowered when he says "No" to selling chocolates, but he loses this power when he follows his violent impulses and punches Emile during the raffle.