The backdrop for A Separate Peace, by John Knowles, is World War II, but it is also a hovering presence in the lives of every character. The teachers at Devon school this year are only old men because the younger men are off to war; all older boys are training for war as well as studying their lessons; the younger boys are trying to act normal in a world which is anything but normal. The relationship between Finny and Gene is a kind of microcosm of the war that is raging in the world outside of Devon school. Even more, once Finny is hurt, a new war rages inside Gene.
There is no exact parallel between the boys and specific countries or people (as is true in works like George Orwell's Animal Farm); however, their relationship is similar to a war. Finny is the boy who goes through life relatively unscathed by everything that happens around him; he is naturally athletic and charismatic, and he loves his life and his friends. His motivations are fairly transparent: he wants to have fun and he wants his friends to have fun with him.
Gene is Finny's roommate; however, unlike Finny, he has to work to achieve his successes (which he does). So much of the time Finny's desire to have fun and include Gene is in direct conflict with Gene's desire or need to study or fulfill his obligations. Gene is resentful about many things: that Finny never gets in trouble despite his consistent rule-breaking, that Finny just assumes Gene wants to do all the things he likes to do, and that Finny is so careless about so many things he thinks are important, like his studies.
This resentment festers and Gene convinces himself that Finny is deliberately trying to sabotage Gene in his endeavors; finally Gene's resentment and distrust erupts in a kind of sneak attack--the first shot in a one-sided war. Both boys are on a tree limb (at Finny's insistence, of course) and Finny wants them to jump together; Gene does not want to do this but has been pressured into this situation. So he takes action:
Holding firmly to the trunk, I took a step toward him, and then my knees bent and I jounced the limb. Finny, his balance gone, swung his head around to look at me for an instant with extreme interest, and then he tumbled sideways, broke through the little branches below and hit the bank with a sickening, unnatural thud. It was the first clumsy physical action I had ever seen him make. With unthinking sureness I moved out on the limb and jumped into the river, every trace of my fear of this forgotten.
Finny has to go home to recover, but the war continues. This war is fought only by Gene as he tries to reconcile what he once believed about Finny and what he now suspects is the truth: Finny never felt anything but loyalty, friendship, and love for Gene, and everything Gene felt was a fabrication created by his own doubts, fears, and unreasonableness.
Finny will never be the same; Gene will do what he can to make it right, but it is a lost cause. Though Finny ultimately forgives him (they come to a rather uneasy truce), Gene does not forgive himself until fifteen years have passed and he returns to Devon school. He knows now that he fought his friend out of fear. He did enlist in the actual war but says,
I never killed anybody and I never developed an intense level of hatred for the enemy. Because 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.