The narrator, Gene, returns to the Devon School in New Hampshire, where he was a student with his friend Phineas 15 years ago, just as World War II began.
The narrative shifts back 15 years, to Gene's days with Phineas. On their first attempt to jump off a huge tree into the river, Phineas, being the daredevil, goes firstand Gene is the only one who follows. Gene is normally a conservative, conformist type person, but around Phineas, he consents to break the rules more often.
Finny is an anomaly at Devon; he is a good student and athlete, but also a charming, likeable rule-breaker. The substitute headmaster, Mr. Patch-Withers, gives a tea for their class. Mrs. Patch-Withers notices that Finny has used the school tie as his belt, which is a heavy offense. Finny concocts some nonsense excuse, at which Mr. Patch-Withers is taken by surprise, and does not punish Finny.
Finny and Gene come up with the idea for a "Super Suicide Society of the Summer Session," a group for exciting and dangerous things. Gene goes onto the diving limb with Finny, and loses his balance; Finny stops Gene from falling, and Gene soon realizes that his friend saved his life.
Some of Finny and Gene's friends begin to join their new club. Finny makes up a game called "blitzball," sort of a variation on rugby and football; the game is a hit that summer.
Finny casually and easily breaks a school swimming record; Finny also refuses to do it again and have it count. Finny proposes that they go to the beach, which means big trouble if they are caught; Gene decides to go along. That night, Finny admits that he considers Gene his best friend, which touches Gene deeply; but somehow Gene can't say the same thing.
Finny mocks Gene's scholarly ambition, and Gene begins to believe that Finny is trying to come out ahead. Finny is the best in the school in athletics; Gene knows that he can be the best in academics, if Finny wouldn't take up so much of his time. Gene finds it hard to compete with Finny, but continues to improve.
When Finny asks Gene to come see a friend jump from their tree the night before exams, Gene vehemently objects. Gene thinks this is Finny's way of trying to sabotage his grades. Finny says he thought that Gene never needed to study. Gene, somewhat appeased, goes to the jumping tree with Finny.
Gene and Finny decide to do jump off the tree together. Once they are on the tree, Gene "jostles" the limb, and Finny loses his balance and falls; Gene seems unconcerned for his friend.
Gene learns that one of Finny's legs had been "shattered" in the fall; Gene grows very guilty about the accident. At last, Gene is allowed to visit Finny in the infirmary. Gene learns that Finny will no longer be able to play sports; Gene cannot believe the news. Gene gets ready to tell Finny the truth; but, he doesn't get the chance, and soon, Finny is sent home to recuperate.
Summer Session ends, and Gene returns home. Finally, he has to go back to Devon; on his way, he goes to Finny's house to see how he is doing. Finny seems weak, like an invalid. Gene tells Finny that he caused the accident, and Finny denies this confession.
Gene is finally back at school, without Finny. Gene got the same room he had during the summer, but no new roommate.
Gene goes to crew practice, which is run by Quackenbush, the uniformly disliked crew captain. Quackenbush immediately challenges him; they have a fight, and both tumble into the water. Gene then quits.
Finny calls Gene long-distance because he was worried that Gene would replace him, though Gene won't. Finny is relieved. When Gene tells Finny that he isn't participating in sports, Finny gets upset; he tells Gene that Gene has to participate for him, and Gene decides to grant Finny this request.
Brinker Hadley starts accusing Gene of arranging Finny's accident in order...