After his return to Devon school and his passage through time in remembrance of his years there, Gene comes to a self-awareness that he did not possess while a youth. Like so many, Gene as a youth has externalized the motives and feelings that he has had, believing instead that Finny was his rival who wished to prevent him from educational success and be more popular and athletic than he. In the end, Gene realizes that Phineas is the only one he has known who possessed no pettiness, no insecurity:
All of them, all except Phineas, constructed at infinite cost to themselves these Maginot Lines [fortifications] against this enemy they thought they saw across the frontier, this enemy who never attacked that way--if he ever attacked at all; if he was indeed the enemy.
While Gene acknowledges that he has killed his enemy at Devon, Phineas was not really his enemy. Wiser, he becomes aware that real enemy has been always within him: the "something ignorant in the human heart." This realization is what gives Gene "a separate peace," a peace apart from the regret of having lost a true friend because of his envy and ignorance.
Depending on your editor, you could receive a variety of answers to this question.
A Separate Peace is one of those coming-of-age novels that reveal truths about humanity we all need to learn. You could argue Gene learns
- about the consequences of his actions (Finny's accident, Finny's not knowing the truth about the accident),
- the power of jealousy (the voice in the writing of the opening chapters demonstrated a real sub-conscious envy of Finny),
- the power of a competitive spirit (Gene wanted to be better that Finny in the classroom, but by the end, Gene lacks motivation for much of anything),
- the problem of trying to fix or remedy past mistakes instead of just receiving forgiveness (Gene tries too hard in some instances to help Finny, the truth might have set him free),
- and the importance of friendship (all characters and situations contribute to this idea in one way or another).
I recommend you pick a topic, then go look for evidence in your text to back it up. The ones I have provided are pretty universal to the book.