The persistent theme of A Separate Peace is the deterioration of a complex friendship. The bond between two boys (Finny and Gene) becomes tested and attacked, as the reader observes a seemingly idealistic relationship fall into failure and declination. Gene becomes challenged with various inner hostilities, while Finny, his freedom for athletics voided, has been forced to find acceptability elsewhere. Furthermore, the book emerges during mid-to-late 1942, during the height of the Axis powers success. The effect of stress and tension on the friendship of the boys becomes elevated. The intensities of war, envy, and complex personalities provide an interesting look into the subconscious mind and insanity of war time youth. .
Phineas and Gene form the illusion of great companionship, combining superior athletic ability with a powerful keenness. However, a silent rivalry develops between them. At the beginning of the story Gene seems to accept Finny's physical agility, but he gradually begins to resents Phineas. As the book progresses, Gene continues to look deeper into their fellowship and quickly becomes wildly jealous of Finny. Eventually, Gene impairs Finny by jouncing the limb where Finny stood. Phineas, meanwhile, seems unaware of Gene's evil thoughts. He continues to remain optimistic. .
Amidst this rivalry, World War II persists and the faculty at Devon School are preparing the students for entrance into the military. Propaganda and the war effort fascinate the youth. From the forming of the Super Suicide Society of the Summer Session, to the shoveling of snow at the railroad yard, everyone is absorbed by the mood of warfare. Gene's realization, while shoveling snow, that "we seemed to be nothing but children playing among heroic men" demonstrated his generation are merely puppets in a global conflict. Gene tolerates his inclination towards pessimism and exposes the evil within him.