Nobody actually has sex in Robert Cormier's frequently banned The Chocolate War. But, there are frequent references to sex, sexuality, and masturbation. But, hey, is that really a big surprise, considering this is a book about teenage guys at a boys' high school?
The novel also raises the issue of homophobia, but doesn't delve into it. On Archie's orders, Emile provokes Jerry to fight by accusing him of being gay. Among other things, Emile tells Jerry "[…] you're a fairy, a queer. Living in the closet. Hiding away" (31.25). Jerry, who appears to be heterosexual, is horrified by the accusation. He thinks, "The worst thing in the world—to be called queer" (31.29).
In the early 1970s when the novel is set, homophobia was the standard. The novel touches on this by showing us both the villains and the hero engaged in homophobic talk and thought. For them, being a gay, is probably the ultimate in "different." Emile tells Jerry, "You're polluting Trinity. You won't sell chocolates like everybody else, and now we find out you're a fairy." (31.29)
Emile, we later learn, has no idea whether Jerry is gay. But, that isn't the point. The point is, Jerry's different from the other boys at Trinity because he refuses to sell the chocolates. At Trinity, anybody who is different, or who fails to conform, is a threat to the power structures in place. Homosexuality is, for many of Trinity's boys, the ultimate symbol of difference. Archie, and to a lesser extent, Emile, understand this fact, and use it to help alienate, intimidate, and provoke Jerry to act against his own best interest.