Gene Forrester, the protagonist, returns to his old prep school, Devon (a thinly veiled portrayal of Knowles' alma mater, Phillips Exeter Academy), fifteen years after he graduated to visit two places he regards as "fearful sites": a flight of marble stairs and a tree by the river that he caused his friend, Finny, to fall out of. First, he examines the stairs and notices that they are made of very hard marble. He then goes to the tree, which brings back memories of Gene's time as a student at Devon. From this point, the novel follows Gene's description of the time span from the summer of 1942 to the summer of 1943. In 1942, he was 16 and living at Devon with his best friend and roommate, Phineas (nicknamed Finny). At the time, World War II is taking place and has a prominent effect on the story.
Gene and Finny, despite being opposites in personality, are close friends at Devon: Gene's quiet, introverted, intellectual personality complements Finny's extroverted, carefree, athletic demeanor. During his time at Devon, Gene goes through a period of intense love for Finny. One of Finny's ideas during Gene's "gypsy summer" of 1942 is to create a "Super Suicide Society of the Summer Session," with Gene and himself as charter members. Finny creates a rite of initiation by having members jump into the Devon River from a large, high tree.
Gene and Finny's friendship goes through a period of intense, one-sided rivalry during which Gene strives to out-do Finny academically, since he believes Finny is trying to out-do him. This rivalry begins with Gene's jealousy towards Finny. This rivalry climaxes (and is ended) when, as Finny and Gene are about to jump off the tree, Gene jounces the branch they are standing on, causing Finny to fall and shatter his leg. Because of his "accident", Finny learns that he will never again be able to compete in sports, which are most dear to him. This leads to Gene starting to think like Finny to try to be a better person and to try to solve some of his envy towards him. The remainder of the story revolves around Gene's attempts to come to grips with who he is, why he shook the branch, and how he will go forward. Gene feels so guilty that he tells Finny that he caused Finny's fall. At first Finny does not believe him and afterward feels extremely hurt.
World War II soon occupies the schoolboys' time, with student Brinker Hadley rallying the boys to help the war effort and Gene's quiet friend Leper Lepellier joining the Ski Troops and becoming severely traumatized by what he sees.
During a meeting of the Golden Fleece Debating Society, Brinker sets up a show trial and, based upon his shaking of the branch, accuses Gene of trying to kill Finny. Faced with the evidence, Finny leaves shamefully before Gene's deed is confirmed. On his way out, Finny falls down a flight of stairs (the same ones Gene visits at the beginning of the novel) and again breaks the leg he had shattered before. Finny at first dismisses Gene's attempts to apologize, but he soon realizes that the "accident" was impulsive and not anger-based. The two forgive each other.
The next day, Finny dies during the operation to set the bone when bone marrow enters his bloodstream and stops his heart during the surgery. Gene does not cry over Finny but learns much from how he lived his life, stating that when Finny died, he took his (Gene's) anger with him. In Finny's death, Gene finally comes to terms with himself.