The phrase "Threads of life changing from schoolboy blue to wartime khaki" in A Separate Peace symbolizes the transition from youth and innocence to the harsh realities of adulthood and war. "Schoolboy blue" represents the carefree life at Devon, while "khaki" signifies military service and the adult world's challenges. For Gene, enlisting offers an escape from guilt and misery, replacing his complex past with the simplicity of military life.

Gene describes his memories of the war years as mostly involving being moved around the United States, learning about new technology and seeking a role in the war effort. He never went overseas or saw combat, as the war was nearing its end. His chief memory is of the journeys across America, suggesting a sense of displacement and lack of direct involvement. The novel emphasizes his friendship with Finny over his war experiences, highlighting individual differences in wartime experiences.

In chapter 13, Gene has a conversation with Brinker Hadley's father and mentions that he has decided to enlist in the Navy, where he hopes to avoid much action and plans to never see a foxhole. At the end of the novel, Gene admits that he never killed anybody during the war or developed an intense hatred for the enemy. Gene elaborates by saying, 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. Given his propensity to harm people like Finny, Gene's comment is ironic because one would expect him to kill an enemy soldier during the war.

Gene measures everything against WWII due to its transformative impact on the world and its symbolic significance. WWII reshaped global economics, ended colonialism, and altered social roles, marking it as the defining event of the 20th century. For Gene, a character in a coming-of-age story, the war symbolizes the ultimate test of character and adulthood. Just as the war changed the world, Gene's experiences at Devon radically transform him, marking his transition from adolescence to adulthood.

Phineas denies the existence of the war in 1943 as a psychological defense mechanism because he cannot participate due to his injury. Once a top athlete, Finny's leg injury, caused by Gene, prevents him from enlisting in the armed forces, which deeply torments him. To cope with his inability to join the war effort, Finny insists that the war is a hoax, a belief he maintains until he admits the truth to Gene.

When Gene says "this wasn't going to be such a bad war," he is engaging in wishful thinking, hoping the war is less dangerous than it seems. This thought arises before visiting Leper, who has gone AWOL. Gene imagines Leper's escape involves heroic deeds, offering him a sense of relief and hope. However, upon meeting Leper, Gene confronts the harsh realities of war, realizing its true formidable nature.

World War II in A Separate Peace symbolizes Gene Forrester's internal and external conflicts. Gene realizes that wars stem from fear within the human heart, much like his own fear that leads him to harm Phineas. This internal war mirrors the global conflict, as Gene's personal battles at Devon School reflect broader themes of envy, resentment, and fear. Ultimately, Gene finds "a separate peace" by confronting these internal struggles, independent of the literal war.

Gene learns that hatred, often tied to jealousy, can have devastating effects, as seen when his brief hatred leads to Finny's injury. His jealousy of Finny's talents causes irreparable harm, teaching him the lethal consequences of envy. Friendship's value is highlighted by Gene's realization of Finny's genuine loyalty, which comes too late. War serves as a backdrop, symbolizing internal conflicts, with Gene concluding that the true battles are within, rather than external enemies.

Leper's evasion of war in A Separate Peace is psychological, as he experiences a breakdown during basic training, while Finny's is physical, resulting from a broken leg. Neither evasion is intentional or their fault. Finny, an athlete, would have been prepared for war physically, but his injury prevents him. In contrast, Leper, more sensitive and academically inclined, is not mentally equipped for the demands of war, highlighting their contrasting experiences.

The war profoundly affects Phineas by shattering his innocence and sense of belonging. Initially, Finny remains detached from the war, viewing it as a distant conspiracy. However, his denial stems from being excluded from military service due to his health, which isolates him from his peers who are preparing for the draft. This exclusion makes Finny feel like an outcast, although Gene suggests he would have befriended the enemy if he had gone to war.