In A Separate Peace, the boys at the Devon School are entrenched in the political climate of World War II, the conflict between good and evil playing out on the global stage, and through Gene, Knowles challenges the reader to transcend the good-versus-evil dichotomy to wonder if there is good on both sides that has simply been warped by unnatural circumstance.
After an escalating series of dares, Gene loses his temper and shakes the tree branch that Phineas is standing on, permanently disabling his supposed best friend. The dichotomy is established; Phineas is good and Gene is evil. Yet as soon as he sets up this comparison, Knowles begins to transcend it. Gene becomes consumed with guilt and confesses his crime to his friend. Phineas refuses to accept that Gene would be capable of hurting him; Gene perceives that this thought alone deeply disturbs his friend and so rescinds his confession. Once Phineas re-breaks his leg, however, Gene comes to him again professing his guilt. Phineas finally accepts it and, after a brief spell of anger, forgives his friend. He understands that Gene acted out of impulse and that his own competitiveness pushed Gene to that point.
After Phineas dies from his injury, Gene goes off to war, carrying the benevolent spirit of his friend with him. He is unable to see the opposing forces as enemies; thinking back on his relationship with Phineas, he decides that competition—in school or in war—makes enemies out of good people. Gene's revelation demonstrates Knowles's ultimate transcendence of the good-versus-evil trope.