Most good stories start with a fundamental list of ingredients: the initial situation, conflict, complication, climax, suspense, denouement, and conclusion. Great writers sometimes shake up the recipe and add some spice.
Initial Situation
Everything is peachy keen in the Summer Session of 1942
Oh sure, there's a world war on and all, but it doesn't seem to be affecting these boys too much. If there's going to be a conflict, it's going to have to be internal, something inside the ideal world that Gene has painted for us as a starting point.
Conflict
Gene harbors feelings of fear and resentment toward his best friend and roommate
This conflict rears its ugly head on the beach, when Gene refuses to return Finny's oh-so-cute "you're my best pal" confession, but we catch glimpses of its ears even earlier in the text. When Gene wants Finny to get in trouble for wearing the tie as a belt, for example, we know that something is up.
Complication
Finny is a good guy
This epiphany only provokes Gene into further jealousy and fear. Not only is Phineas a better athlete and world-class troublemaker, but he's also a bigger person than Gene. This is more than a sixteen-year-old with dubious self-awareness can take.
Climax
Finny's fall
We've been building towards some large-scale manifestation of Gene's animosity for a while now. And Knowles certainly delivers. This is not only the climax of the plot, but also the most emotional and psychologically scrutinized moment of the text. Everyone will be talking about it for the next year and 150 pages, we swear.
Suspense
Will Gene be found out?
This stage lasts for a solid chunk of the novel. Gene lives in perpetual fear that someone will find out he caused the accident, that Brinker will make his joking accusations serious, that Finny will know the truth, etc. But there's added suspense since we don't actually know for sure whether Gene intentionally jounced the limb. We're not sure if it was an accident, if it was subconscious, or if it was purposefully malicious. And Gene doesn't seem too sure either.
Denouement
Finny falls down the stairs; people stop pestering Gene; Finny dies
When Finny tells Brinker off and leaves the Assembly Hall, the novel's big suspense scene is over. Finny's fall means that no one's going to be concerned with what happened a year ago, and Finny's death only secures that fact. The last conversation between the boys is the real meat of the denouement, however, since everything comes to light. Finny finally faces what happened in the tree, he admits his true feelings about the war, and Gene gives him a great little speech about the nature of his character and its incompatibility with fighting.
Conclusion
Chapter Thirteen
Gene's musings in Chapter Thirteen draw the purse-strings neatly on the novel. He ties together the novel's themes and draws a variety of conclusions concerning Phineas, war, Brinker, and the nature of the universe. Honestly. We promise. Go read your book.