At the end of the book, Gene explained that most people came up against something in their lives that tested them to the max, and broke them, "and they were not the same again." For most characters in this story, it was the war. Once they realized that there was "this overwhelmingly hostile thing in the world with them," they broke, changing forever. However, for Gene, the real war that he went to fight in was never a problem for him. He had already confronted his own private war, in the form of his jealousy for Finny, and how his body instinctually reacted to that jealousy, and then dealing with the repercussions of that action. He had to look his meanness in the face, own up to it by confessing it to Finny, then watch in despair as that meanness took the life of one of his best friends. His war was overcoming his distaste of himself and his cowardly actions in regards to Finny. He had to struggle each day with the knowledge that his jealousy of someone had led him to essentially destroy someone, someone who could not be destroyed in any other way.
This battle against other people, against our own insecurities, and against our own more base tendencies is something that young people fight every single day. Young people constantly pit themselves against other people that they desire to be like, and against their own worst traits. They focus and dwell on them, and until they can learn to be confident as they are, and who they are, no matter who surrounds them, they do not win that battle.
I hope those ideas help, and that they give you some food for thought. Good luck!