The irony of Gene's war is that it does not involve World War II. Gene enlisted in the Navy and was headed to Pensacola, Florida for training after he graduated from Devon School. He hoped this would mean lots of time in training and avoidance of "a foxhole."
Gene's war was within himself. His war was the battle he fought against his jealousy (and hatred at times) of Finny, his anger with himself, and the way in which he had betrayed Finny but was unable to face up to it and confess it. Gene didn't fight a German, Italian, or Japanese enemy in his war. He didn't fight against the expectations of the older generation, as did Brinker against his father; he didn't battle against society in general, as did Quackenbush. As Gene came to realize,
my war ended before I ever put on a uniform; I was on active duty all my time at school; I killed my enemy there.
He killed his enemy by finally, with time and maturity and distance from the events, achieving his separate peace within himself.