A Separate Peace explores not only military warfare (it takes place during World War II), but personal wars. Feelings of hostility, resentment, and fear dominate even what should be the most peaceful of environments. The novel claims that we all identify enemies in the world around us, that we "pit ourselves" against them so as to have an object for our hate and fear. Wars, both personal and political, are thus "the result of something ignorant in the human heart," an inability to understand the self and others.
Gene's relationship with Finny is an allegory for World War II.