Set against the backdrop of World War II, A Separate Peace explores morality, patriotism, and loss of innocence through its narrator, Gene Forrester, in his relationship with classmate and friend Phineas.

Gene Forrester returns to his old prep school, Devon (a potential reflection of Knowles's real life alma mater, Phillips Exeter Academy),[1] 15 years after he graduated, to visit two places he regards as "fearful sites": a flight of marble stairs, and a big tree by the river.

Finny creates a rite of initiation by having members jump into the Devon River from a large tall tree.

Gene is even more resentful of how Finny frequently breaks rules and gets off easy, because of his charm and the school staff being too occupied with the war effort to notice or care.

World War II soon occupies the boys' time, with fellow student Brinker Hadley rallying the boys to help the war effort and Gene's quiet friend Leper Lepellier joining the Ski Troops, which leads to him getting discharged from the military under Section 8 due to being unable to sleep during basic training.

During a meeting of the Golden Fleece Debating Society, Brinker sets up a show trial of sorts and, based upon his shaking of the branch, accuses Gene of trying to kill Finny.

Other themes exist as part of Gene's consciousness and his relationship with Finny, such as the threat of codependency and the creation of inner enemies.

That is furthered by the characters' notion that World War II is merely a conspiracy, which creates a private illusion in which both Finny and Gene can exist together.

This symbolises innocence and youth, which is "lost" when Finny falls from the tree, giving lead to the Winter Session.

[4] Various parties have asserted that the novel implies homoeroticism between Gene and Finny, including those who endorse a queer reading of the novel and those who condemn homosexuality as immoral.

For example, the book was challenged in the Vernon-Verona-Sherill, NY School District (1980) as a "filthy, trashy sex novel"[5] despite having no substantial female characters and describing no sexual activity.

Though frequently taught in US high schools, curricula related to A Separate Peace typically ignore a possible homoerotic reading in favor of engaging with the book as a historical novel or coming-of-age story.

[6] Knowles denied any such intentions, stating in a 1987 newspaper interview:Freud said any strong relationship between two men contains a homoerotic element...