In A Separate Peace, the war symbolizes on a grander scale the same evil that drives Gene's private evil. Thus, it symbolizes a war of jealous rivalry.
Shortly after he comes to Devon School, Gene becomes convinced that his roommate Phineas keeps him from his studies so that he will not excel. Gene feels that there is a "deadly rivalry" between Phineas and himself and is sustained on this idea:
The thought was, You and Phineas are even already. You are even in enmity. You are both coldly driving ahead for yourselves alone. . .... I felt better. We were even after all, even in enmity. The deadly rivalry was on both sides after all. (Ch.4)
Gene, then, convinces himself that Finny (Phineas) does not want him to succeed in his academic work, just as Gene does not want Finny to be superior in athletic activities. In truth, however, it is only his envy of Phineas that has caused this private war, an evil which motivates Gene to jounce the limb of the tree, bringing about Finny's loss of balance and fall which breaks his leg. Later on, Gene realizes that Finny has never envied him, and Gene's jealousy becomes even more bitter as he senses the moral superiority that Finny possesses.