Gene Forrester, a man in his early thirties, returns after fifteen years to his prep school, the Devon School of New Hampshire. He stops at Devon's main building and then walks down to look at a large tree by the Devon River
The story shifts to 1942. World War II rages overseas, and the smart and careful Gene and his carefree and athletic roommate Finny are students at Devon's summer session. One day, Finny, Gene, and some other students hang around a big tree by the river. Finny climbs the tree and jumps into the river. Gene, though terrified, follows. Later that day, the two boys form a club, which they name the Super Suicide Society of the Summer Session. One of the rites of passage for joining the club is jumping out of the tree by the river. As summer continues, Gene and Finny grow closer. Yet Gene also begins to feel a deep rivalry with Finny. He envies Finny's athletic prowess, and suspects Finny has been trying to sabotage his academic success. At one meeting of Gene and Finny's suicide society, Finny proposes that he and Gene perform a simultaneous jump from the tree. As they both stand ready to jump, Gene shifts and shakes the branch. Finny falls to the ground, shattering his leg and his athletic career. Gene tries to confess to Finny what he did, but can't make himself do it before the summer ends.
On the way back to Devon in the fall of senior year, Gene visits Finny and confesses that he caused Finny's fall. Finny refuses to believe him. Gene returns to Devon and finds that the laxity of the summer session has been replaced by the strict rule of the regular masters. The senior boys' consciousness of the war also increases, and soon a boy named Brinker Hadley influences Gene to enlist, until Finny returns to school and convinces Gene not to. Everyone is shocked, however, when a dreamy boy named Leper Lepellier does enlist and leaves school.
Gene has decided that pursuits like sports feel trivial in light of the war, but Finny argues that war is just a creation of fat old men who want to control the younger generation. Soon Finny convinces Gene to start training for the Olympics—a dream that used to be Finny's. As Gene's training intensifies, the two boys regain their closeness and Gene gains a sense of internal peace that he's never before experienced. One day, Finny proposes that the boys hold a Winter Carnival. It's a great success, until a telegram arrives for Gene from Leper. Leper has deserted the military in order to avoid getting discharged for insanity. Gene goes to Leper's home in Vermont, where they have an argument in which Leper really does seem half-insane and accuses Gene of willfully causing Finny's fall.
Back at Devon, Brinker begins to question why Gene hasn't enlisted and suspects it has something to do with Finny's fall. Finny also spots Leper skulking around the school. One night, Brinker and a few other students round up Gene and Finny and hold a mock trial to investigate Finny's fall. They bring in Leper as a witness. He testifies that Gene caused Finny's fall on purpose. Finny stands up and shouts that he doesn't care either way. He storms out and falls down a nearby set of stairs and re-breaks his leg.
Gene tries to visit Finny at the infirmary, but Finny is furious at him. Gene spends the night wandering the campus and feeling as if he doesn't exist. The next morning he again visits Finny, and together the two boys agree that Gene's actions at the tree were not purposeful. Finny dies that afternoon, when some marrow from the break gets into his blood. Gene doesn't cry when he hears this, or at the funeral. He feels that Finny is now a part of him. The boys all graduate, and enlist in various safe branches of the military. Gene never sees active duty, but feels he fought his own war at Devon and that he understands the hatred all men harbor in their heart—all men, that is, except Finny.