Chapter 1: The narrator (Gene) returns to the Devon School in New Hampshire, that he graduated from 15 years earlier. He goes to a certain tree and switches back to the past. Phineas dares everyone to jump from a branch in the tree into the river. Phineas, and Gene both jump. On the way back Phineas and Gene play fight so that they are late for dinner.
Chapter 2: Mr. Prud’homme, a master, stops by the boys’ room to scold them for missing dinner again for the ninth time in two weeks. Phineas explains that they were late because they were jumping out of the tree to toughen up for the war. Mr Prud’homme, accepts the explanation because, he, and everyone else, feel sorry for the boys that will soon have to go to war.
Chapter 3: The boys join The Super Suicide Society of the Summer Session. The club meets every night. Phineas and Gene open each night by jumping out of the tree. They make a new kind of war game called blitzball, in which everyone is everyone else’s enemy. Phineas breaks the schools swimming record, but tells Gene not to tell anyone, he just wanted to do it for himself. Gene and Phineas of campus to the ocean to swim. They have a drink at the bar, the spend the night on the beach, and Phineas tells Gene he is his best pal. Gene is not sure if he feels the same.
Chapter 4: Gene and Finny (Phineas) wake up and head back to Devon. Gene fails his trigonometry examination for the first time. Finny tells Gene that he studies too much. Gene thinks Finny is jealous. Gene wants to earn the Scholastic Achievement Citation to get even with Finny. Gene knows that Finny must be best and that he cannot be best if Gene becomes even with him through his studies. Gene decides that he and Finny are locked in a complete enmity rather than friendship. Finny announces Leper’s intention to jump from the tree and coazes Gene away from his studies. Gene and Finny are going to jump together, Finny falls to the ground, and then Gene jumps into the river.
Chapter 5: Finny has a shattered leg. Gene bears private guilt. He puts on Finny’s clothes and the sensation excites him. Dr. Stanpole, the school physician, informs Gene that Finny wants to see him. Finny recalls the fall, and expresses that he thought Gene wanted him to fall. Gene is about to confess when Dr. Stanpole interupts. Finny is taken to his home near Boston and Gene returns to his hometown in the South. In September, Gene stops by at Finny’s home. They talk about the summer and Gene confesses that he caused Finny’s accident. Finny replies that Gene is crazy and had done no such thing.
Chapter 6: Gene begins work as assistnt crew manager, even though he has never managed sports before. The crew manager Quakenbush refers meanly to Gene as being “maimed” and Gene attacks him as a reply. Gene is scolded by the master for gambling during the summer, and other infractions. Finny phones Gene and, after ascertaining that they would be roommates when he returned, becomes angry at Gene for being a crew manager rather than actually playing the sports. Finny explains the Gene must play sports for him. Gene realizes that he was meant to be a part of Finny from the beginning.
Chapter 7: Brinker Hardley stops in to see Gene and congratulates him for having been able to secure a whole room for himself. He suggests that Gene accompany him to the butt room (smoking room). Gene is teased about having done away with his roommate. Gene is serious, but then soon starts to joke to. Brinker composes a poem pointing that war is boring, and Devon continues in peace. Many of the Devon boys volunteer to shovel snow out of the railroad tracks. Brinker announces that he is enlisting. Gene thinks about enlisting as well, but his thoughts are put on hold, when he returns and find Phineas waiting for him.
Chapter 8: Gene explains to Finny that there are no maids because of the war. Finny has a quiet vision of peace. Finny begins to coach Gene in preparation for the 1944 Olympics. Finny is convinced that there really is no war at all. He thinks a bunch of fat men fabricated the whole idea of a war. Gene tries to forget about the war and concentrate on the Olympics. Mr. Ludsbury explains that all exercise is really part of the war effort.
Chapter 9: The boys have returned from Christmas vacation. Leper Lepellier enlists in the ski troops. Gene reacts that war must be unreal for a peaceful Leper to enlist. Finny tries to draw Gene into a private world with just them two. Finny comes up with a plan for a winter carnival. Finny establishes a separate peace for the boys at Devon. A telegram arrives from Leper, saying that he has escaped and needs help. The boys are forced to realize that war has broken in upon them at last in a real and important way.
Chapter 10: Gene recollects preparations for war undertaken by himself and others his age. Most of his time was exhausted in traveling around aimlessly to different places until the war was suddenly and prematurely brought to a halt by the dropping of the atomic bomb. He is en route to visit Leper. Gene thinks Leper is a “physco”. Leper explains that the army was going to dismiss him with a Section Eight (the nuts and physco’s in the service dismissal). Leper says that Gene is “savage underneath,” and then supports his view by citing the way Gene knocked Finny out of the tree and “crippled him for life.” Gene reacts angerly, but Leper’s mother enters. They have lunch, and then take a walk in the country. Leper recalls some of military life. Gene screams that he doesn’t care about what Leper is saying because it has nothing to do with him.
Chapter 11: Gene returns to Devon and finds Finny in a snowball fight. The fight rages as war games. Finny is sobered and while saying that htere is no war shows that he knows that the war really does exist. Binker tells Gene to stop pitying Finny, because Finny will start pitying himself. Brinker points out that it would be good for Gene if everyone could forget about Finny’s accident. Finny confesses to Gene that he is no convinced that the war is real, and also explains that he has seen Leper hiding in various places around the school grounds. Brinker conducts a war trail, investigating the cause of Finny’s accident and ambiguously accusing gene as the guilty party. Brinker asks Finny to recall the events leading up to his actual fall and slowly it becomes evident that Gene was up on the branch with Finny. Finny tells the boys that Leper is on the school grounds. Leper is brought to trial as a key witness who had been present when the accident occurred. Leper says he had seen both boys in the tree, looking “as black as death” against the bright sun behind them. Finny ends the trial by rising angrily, cursing at Brinker, and for the first time starting to cry. Finny falls down the stairs.
Chapter 12: Phil Latham, the wrestling coach, is brought to the scene of the accident and malkes finny lie still until Dr. Stanpole arrives. Finny’s leg has a clean break this time. Mr. Ludsbury orders Gene to his room. Gene sneaks around to the infirmatory were Finny will be taken. Dr. Stanpole arrives and takes Finny in his car. Gene talks to Finny through the infirmatory window, explaining that he wants to help, but Finny remains angry and unreceptive. Gene sleeps at the stadium. He finds a note in his room from Dr. Standpol, requesting Finny’s things be brought to the infirmatory. Finny finally admits Gene’s innocence. Finny knows that Gene did not push him ot of the tree on purpose. Finny is very unhappy though. Finny wants desperately to be in the war. Dr. Stanpole announces that Finny is dead. Dr. Stanpole loses control of himself as he tries to explain that some marrow from the broken bone must have been released into the blood stream and gone to the heart, killing Finny immediately.
Chapter 13: The Far Common of the Devon School is being taken over by the army. Gene realizes that no one has accused him of being responsible for what happened to Finny. Mr. Hadley, Brinker’s father, arrives, and lectures the boys on bravery, heroism, and the importance of a military career. He is disgusted that Gene says he hopes he never sees a foxhole. Brinker himself cannot accept his father’s mindless announcement that everyone should be willing to die for his country. Gene realizes that wars are caused by “something ignorant in the human heart.” He realizes also that the hard part of the war is over for him; he endured it at Devon. For the real horror of war is slowly mitigated through the difficult period of preparation of war, not through actual war experiences.