How has Gene from A Separate Peace fought a self-imposed internal battle all along, and who was his true enemy?
Gene believes when he first arrives at school and observes Finny's popularity and charisma that he must compete with Finny. This misidentification of his "enemy" or competition causes Gene to act irrationally--believing that he hates Finny and jouncing the tree branch so that Finny falls. In reality, as Gene discovers after Finny's death, he does not hate Finny; he hates the part of himself that is not like Finny. He is an outsider at Devon School because of his family background and home state and longs to fit in. He thinks that he needs to become Finny in order to do so instead of focusing on his own gifts (academics).
At the end of the novel, Gene narrates (as an older man) that he had to find a separate peace within himself. While World War II raged on around the boys at Devon, Gene's internal war was raging inside himself, and he only "signs a treaty of peace" with himself when he realizes that Finny was a good friend all along and that he needed to be content with who he was. Finny helps Gene recognize this not only through his forgiveness but also by showing Gene that he was struggling himself (he wrote to every nation he could think of, trying to get accepted into their armies).
Gene's struggle is commonly referred to as teenage angst, because as teens, many are searching for their identities, and it is difficult not to let others impose on one's self who they think an individual should be.