One of the biggest underlying themes in A Separate Peace is that despite the seemingly playful attitude at Devon, and likewise apparent esprit de corps between Phineas and himself, Gene is a tortured individual at his core. At the beginning of the book he tries to be a good friend, and give the benefit of the doubt in most situations, while at the same time struggling to keep his own life in line and interests protected. This lifestyle eventually takes its toll on him, and he comes to resent Finny because Finny is better. Nothing more, nothing less needs to be said; he's just better. Because of this Gene begins to hate him for being better not only at sports, but he is more well liked, happier, but most of all, a better person - a better friend. Though he tolerates it at first, this knowledge is ultimately too much for Gene to bear; it frustrates him like nothing else, because he knows he couldn't possibly measure up to his best friend. This evokes a running conflict inside of him: a schism is struck between two sides of his personality - Gene, friend of Phineas Vs. the monstrous conspiratorial Beast of Jealousy.
By degrees the monster wins the war, and as a result drives Gene to trounce the branch and end Finny's athletic career permanently. He feels guilty but doesn't know what can be done, whether he is even responsible. It's debatable whether we can call it an accident, whether it was his fault- after all, we can't control (or suppress) our subconscious urges, but they are as much a part of us as our flesh and bones. For a long while he intends to hide the truth from everyone around him, but no one so much as suspects him at first. Since he has no accusations from which to defend himself, the guilt eats at him even more, because he has nobody to even profess his innocence to, he's just left to the silent mocking of his own mind.
Finally, when he goes to visit Phineas in the hospital, he resigns himself to telling his friend the truth, “that's what Finny would have done in my place,” he decides. This mollifies Gene's guilt somewhat, and consequently strengthens their friendship via his willingness to speak to Finny again. Coupled with the passage of time, which is this case heals wounds both physical and spiritual, the increased honesty between the two of them goads Gene to try to make it up to him, in a sense. For example, he tolerates and to a point believes Finny's drivel about the war being a hoax, if only as a show of goodwill. He begins to feel better about the whole situation, and life in general, and starts to believe that maybe things will turn around for him.
However, these hopes are crushed by the “trial” because Gene knows that under the combined duress of Brinker and all his minions, Phineas will eventually succumb to the allegations against his best friend. After he is forced to accept reality, he cannot cope with it. He was too much of an idealist for this world, and in the end it killed him. The world had beaten down upon him. The same is true of Gene, really. The very occurrence of the accident killed his optimism, so that he was rendered unsuitable to face reality, a fact that haunts him for fifteen years. It is not until he returns to Devon that he can shake off the fog of guilt that has so thoroughly consumed his mind.
When Gene does return to Devon, he is finally able to face his demons, and forgive himself for what he's done. He had made peace with Finny long ago, but still blamed himself for all that had happened. I think in this case it's true that we are our toughest critics, because we can regret the deeds we've committed. Therein lies the difference- we do not feel bad about being wronged, we don't regret it. The people we hurt may give us their blessing, and we accept it, but the fact remains that they feel no lament, as there was nothing they could have done differently. In this respect we are certainly harder on ourselves than we need to be, a lesson Gene learned the hard way. I think ultimately we sometimes need to just come to terms with our faults and move on. If he had, in the very beginning, he could have had a very different life- one of tranquility, and his own internal separate peace.
