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 to get a room to himself. Brinker's accusations, though out of nowhere, trouble Gene a great deal.
Fall passes, and the war remains distant. The first snow falls, and soon Gene and the boys spend a miserable day at the railroad yard, shoveling snow. Soon, enlistment fever hits a few of the boys, especially Brinker and Gene. Gene feels that enlisting will give him a sense of purpose. But, then he goes back to his room, and finds Finny there; suddenly, he has a purpose to stay at Devon again.
Gene is surprised at Finny's sudden return; Finny looks well again. Gene is happy that Finny is back; however, he is still paralyzed by guilt. Brinker reintroduces his insinuations about Gene causing Finny's accident, but Finny doesn't want to think about it. Finny is not pleased with the idea that Gene might enlist; Gene immediately brushes aside any talk of him enlisting , reassuring Finny.
Finny is upset because Gene isn't doing sports like he promised; Finny goes off on a rant about how the war was designed to keep people in their place. Gene doesn't believe him, and asks Finny how he knows all this stuff that nobody else does; Finny then says "because I've suffered," opening another big, painful can of worms (109).
Finny and Gene never talk about Finny's little show of bitterness again. Finny says he wants to coach Gene for the 1944 Olympics; Gene knows there won't be any Olympics due to the war. Gene learns to be a little more skeptical of how the teachers manipulate the war to try and get the boys to behave.
Gene and Finny keep training, doing long runs in the morning; Gene thinks he can't do them, until one morning he just amazes himself and it comes naturally to him, just as it did with Finny before.
Leper is convinced by a video of American ski troops that he must enlist; Leper leaves a school week later, the first of Gene's class to enlist. Leper becomes a symbol of the war for the boys; he is the fantastic liason between them and the newspaper reports they read everyday. Phineas pulls away from his friends because of their fascination with the war. Finny tries to draw Gene away with him, into Finny's little world where war and enlistment do not exist.
Finny decides to organize the first winter carnival at Devon, so that there's something fun to do outside; Gene is persuaded to help. The carnival comes; Brinker has obtained some hard cider, snow sculptures have been made, and prizes are all set up. Finny is definitely cheered up by the whole little festival, and the other boys are happy for the break.
Then, a telegram comes for them from Leper; he says he has "escaped" from the army; Finny and Gene are shocked, and are determined to find Leper.
Gene goes to see Leper at his home in Vermont, and Leper is very different. Leper accuses Gene of causing Finny's accident, and reveals that he left the service because he was about to be discharged for mental health reasons. Gene gets angry and attacks Leper for his comments, then apologizes and is too embarrassed to leave immediately. After lunch, Leper and Gene go for a walk, and Gene sees that Leper really has cracked up. Leper talks nonsense, and somehow it affects Gene, who runs away from Leper.
Gene is finally back at school, and gets caught in a snowball fight. Brinker finally gets the truth about Leper out of Gene; Finny reveals that he's finished with his fake-war pretense. Devon again becomes swept up by the war and patriotism.
Brinker confronts Gene again about Finny's accident, and says they should get everything into the open, which Gene disagrees with. Later that night, Brinker drags Gene and Finny to the First Building. Brinker is holding some kind of inquiry into the accident; Brinker brings Leper, who was at the scene of the accident, out to speak. When Leper says that Gene did indeed push Finny, Finny freaks out and runs from the room. He falls on the marble steps outside, and re-breaks his leg.
The others rush out to help Finny; someone goes to fetch Dr. Stanpole. Finny is driven by Dr. Stanpole to the infirmary. Gene decides to go to the infirmary and see how Finny is. Finny is angry at Gene, and falls out of his bed while trying to get up and come at him; Gene says he's sorry, and leaves.
Rather than going home, Gene walks around the stadium and the gym; he is in a strange sort of reverie, where he feels like a spirit, and everything around him is vibrant and full of meaning. Gene goes to the infirmary to take some of Finny's things; Finny asks Gene if he had made him fall out of the tree because Gene hated him. Gene reassures him that it was some blind unexplainable thing that made him do it, and it had nothing to do with hate or any ill-will against Finny. Finny says he believes Gene, and they finally reach closure with that issue.
When Gene returns to the Infirmary to see Finny after his operation, he meets Dr. Stanpole. Dr. Stanpole sits him down and tells him that Finny died during the operation. Gene is too shocked to even think about it, and cannot cry because he feels like he died too, along with his friend.
It is June, and Devon gives use of the Far Common to the war effort. Brinker and Gene watch the troops and jeeps and equipment being brought in, for a Parachute Rigger's School being made there; Brinker brings up Leper, which Gene tells him not to talk about. Gene says that no one blames him for what happened to Finny, although he blames himself.
Gene is introduced to Brinker's dad, and says that he has joined the Navy. Brinker has joined the Coast Guard, probably part of his scheme to stay out of battle. Brinker's dad is very gung-ho about the military, and gives the boys a speech about having a good military record, and how people will respect them based on what they did for the war. Brinker obviously doesn't agree.
Gene then talks about Finny, and his experience in the war; how Finny was the only person he knew whose character was safe from being corrupted by the war, and how his friendship with Finny prepared him for his own experience. In lieu of Finny, he has finally adopted Finny's way of looking at things, and some of Finny's personality and rebelliousness. Finny means a lot to him and still influences him, and Gene is finally able to appreciate his friend for all that he was, and make peace with him.