A Separate Peace spends a lot of time talking about the war, and as much time talking about sports. At first these seem like completely different things. Sport is, as Finny sees it, "purely good," whereas war is destructive and, as Gene says, caused by "something ignorant in the human heart."
Of course, the kicker is that, at least for the boys at Devon, the war holds strange parallels to sport. Their eagerness to enlist suggests a misguided understanding of warfare as the ultimate game. Phineas, the master of all sports, is devastated to discover he can't be part of the fun. Of course, the novel argues that war is purely evil, as opposed to purely good fun and games.
Once you start looking, you see the idea of sport cropping up all over the place at Devon, from Finny's purely innocent Blitzball to the rivalry Gene establishes between himself and Finny – a rivalry that proves itself to be deadly. As peace deserts Devon, as the boys move from their youth to adulthood, sports are perverted from their once "purely good" form and take on warlike traits. No better example exists than Leper's obsession with skiing. Once a solitary and reflective afternoon activity, skiing is taken over and made into an instrument of war. There's also the idea of the Olympics; Finny tries to use sport to compensate for not being able to participate in war. And don't forget the tree incident itself – a devastating, warlike perversion of what was once purely good, tree-jumping sport.