A Separate Peace Gene Forrester is a quiet, intellectual student at Devon School in New Hampshire. During the Summer Session of 1942, he becomes close friends with his daredevil roommate Finny, who has a talent for getting away with mischief through his sincere, disarming charisma. Finny prods Gene into making a dangerous jump out of a tree into a river, and the two start a secret society based on this ritual. Gene envies Finny's astonishing athletic abilities, and he begins to suspect that Finny envies his superior academic achievements and has been taking steps to distract him from his studies. His suspicions turn to hatred, but he makes sure to maintain an appearance of friendship so Finny will not suspect him. Gene realizes he was grievously mistaken about the existence of any rivalry between them one day when Finny expresses a sincere desire to see Gene succeed.

He goes to the tree to jump with Finny while he is still in a state of shock from the force of his realization, and when Finny gets out to the edge of the branch, Gene shakes it, causing Finny to fall to the bank and shatter his leg. The doctor tells Gene that Finny's athletic days are over. Gene goes in to see Finny and begins to confess what he has done, but the doctor interrupts him and Finny is sent home before Gene gets another chance. The Summer Session ends, and Gene goes home for a brief vacation. On his way back to the school from his home in the South, Gene stops by Finny's house and confesses that he shook the branch on purpose. Finny refuses to listen to him, and Gene takes back his confession and continues on to school.

World War II is in full swing, and the boys at Devon are all eager to enlist in the military. A prominent class politician, Brinker Hadley, suggests to Gene that they go off to enlist together, and Gene agrees. That night he finds Finny has returned to school, though, and he drops his plans to enlist, as does Brinker. Finny expects Gene to take his place as the school's sports star, and when Gene protests that sports no longer seem important in the midst of the War, Finny declares the War is all a massive hoax. Finny tells Gene he once had aspirations to go to the Olympics, and Gene agrees to train for the 1944 Olympics in his place. Everyone is surprised when a gentle, naturalistic boy named Leper Lepellier becomes the first one in their class to enlist.

Gene and Finny go on training, shielded within their private version of world events. During a winter carnival Finny has organized, a telegram arrives for Gene from Leper, saying he has escaped and desperately needs him to come to his home in Vermont. Gene goes and finds that Leper has gone slightly mad. Leper, who was present at Finny's accident, reveals that he knows the truth about what happened. Gene becomes frightened by Leper's ranting because of its possible implications for his own reactions to military life, and he runs away back to Devon. When Brinker hears of what has happened to Leper, he laments in front of Finny that Devon has already lost two of its potential soldiers.

Gene, afraid that Finny will be hurt by this remark, tries to get him to launch into his hoax story again, but Finny lays it to rest. Brinker has always harbored suspicions that Gene had something to do with Finny's accident, and in an attempt to dispel them once and for all, he organizes a midnight tribunal of schoolboys and has Gene and Finny summoned without warning. They question the two about what happened, but Finny is too confused about the whole thing to speak conclusively, and Gene maintains he does not remember. They bring in Leper, who was seen earlier that day skulking about the bushes, and he begins to implicate Gene in causing the accident. Finny declares he does not care about the facts and rushes out of the room. He falls down the stairs and breaks his leg again.

Gene sneaks over to the Infirmary that night to see him, and Finny sends him away angrily. Gene wanders the campus until he falls asleep under the football stadium. The next morning, he goes to see Finny again and tells him he is sorry and that his action did not arise from hatred. Finny accepts this explanation and the two are reconciled. While the doctor attempts to set Finny's leg, a piece of marrow detaches from the bone and stops Finny's heart, killing him. Gene does not cry when he hears the news, because he feels he has become a part of Finny and will always be with him.

The boys graduate and go off to enlist in relatively safe branches of the military; Gene is glad that at least his coming regimentation will not take place at Devon, where he spent his idyllic summer.