The Different Rules of Summer
15-year-old Aristotle "Ari" Mendoza has no plans for the summer of 1987. He is bored, miserable, and friendless. Ari lives with his mother and his father; his two older sisters have grown up and moved away and his older brother is in prison. Everyone in Ari's family refuses to talk about his brother and behaves as if he were dead. Ari's father served in the Vietnam War, but also refuses to talk about his experiences in battle. Ari goes swimming to escape the suffocating silence of his house, even though he doesn't know how to swim.
At the pool, a boy named Dante Quintana offers to teach Aristotle how to swim. The boys bond over their classical names and eventually become inseparable. Ari is fascinated by Dante's swimming ability as well as his sincerity. Dante teaches Ari about literature and poetry. He hates to wear shoes and struggles regularly with his Mexican identity. Aristotle is astounded by the affection displayed by Dante's family because he feels so distanced from his own parents. Aristotle goes with Dante and his parents to the desert so that they can look at the stars, where Dante proclaims "Someday, I'm going to discover all the secrets of the universe." One afternoon, the boys see some children shooting birds with a BB gun. Dante and Ari confront them, take away the gun and bury the sparrow the children shot.
Sparrows Falling From the Sky
The morning after they bury the sparrow, Ari wakes up with a terrible case of the flu. He has fevered dreams where he is in the rain and searching for Dante and his own father. He also has dreams where his imprisoned brother, Bernardo, is across a large river while Ari calls for him to return. Ari's father and mother nurse their son back to health, but his bad dreams persist.
Dante sketches Ari while he recovers over the next several days. He refuses to show Ari his sketchbook, but leaves Ari a lifelike drawing of a chair as a gift.
When Ari feels better, Dante tells Ari that he and his family are moving to Chicago for the next school term because his father was offered a new job. The same day that Dante announces his move, the two boys see a bird lying injured in the road. While Dante goes into the road to check on the bird, a car speeds around a corner. Ari dives into the street, pushes Dante out of the way, and is hit by the car. While Dante leaves almost unscathed, Ari is hurt very badly.
The End of Summer
Both of Ari's legs and his left arm are in casts. Dante only suffers minor injuries and is overcome by guilt. Ari makes his friend swear not to talk about the accident, thank him, or cry. Ari is angry when Dante cries because he believes that he should be the one crying. Following the accident, the Quintanas and the Mendozas grow closer. Both boys' mothers talk more frequently and share ideas about their sons. Dante's mother sends him to a therapist to talk about the incident.
Dante visits Ari in the hospital. He brings two novels, War and Peace and The Grapes of Wrath. He also gives Ari his sketchbook, the first time he has shown anyone the book. Ari is sickened by the gesture, because he believes Dante gives him the book because he feels as if he owes Ari for saving his life. He throws the book against the hospital wall and refuses to look at it.
After the incident, Ari's mother suggests that he also see a counselor. Ari lashes out and insists that he will see a therapist when she starts talking about his brother. Ari's father also visits him in the hospital every evening. Ari reads The Grapes of Wrath and his father reads War and Peace. When Ari is allowed to come home, he and his father continue to read together. Ari believes their silent reading is their own way of talking.
Three weeks after the accident, Ari's father offers to buy him a car for his upcoming birthday. Ari asks for an old pick-up truck. Gradually, Ari heals and is able to bathe himself and write again. The improvement makes him happier, but he still feels suffocated in his own home and he dreads the start of the school year with Dante's absence.
Before Dante leaves for Chicago, he reveals the two things he loves most in the world are swimming and Ari. However, Ari says that he shouldn't tell him those things, even if they are true. The two boys promise each other that they will still be friends when Dante returns in the summer.
Letters on a Page
When school starts again, Ari is reluctant to tell his schoolmates about the accident. Two girls from his class, Gina Navarro and Susie Byrd, hound him for answers.
Meanwhile, Ari's father gives him a 1957 Chevy pickup truck. He decides that when his casts come off, the first place he will drive is to the desert where he can look at the stars. Ari also becomes infatuated with Illeana, a girl from his school. He becomes intent on kissing her.
Dante sends Ari several letters. In them he speaks about how he goes to parties, tries marijuana, drinks alcohol, and kisses girls. He also talks about visiting the Art Institute of Chicago where he sees one of his favorite paintings, Nighthawks by Edward Hopper. In his later letters, Dante confesses that he'd rather be kissing boys than girls. The day Ari gets his casts off, he takes a walk by Dante's house. He finds a stray dog, whom he takes home and names "Legs".
Ari's life without Dante revolves around learning to drive, lifting weights, running with Legs, trying to find information about his brother at the library, arguing with Gina and Susie, trying to run into Ileana at school, reading Dante's letters, having bad dreams, and working a part-time job at a burger joint called The Charcoaler. He writes this list down in his journal.
Over Christmas break, Ari finds an envelope in his house marked "Bernardo." Ari knows that the envelope contains everything he wants to know about his brother, but he is afraid to open it. On New Year's Eve, Susie and Gina invite Ari to a party where Ileana gives him his first kiss. In the weeks after, though, Ileana tells Ari that she doesn't want to go out with him because she already has a boyfriend who is in a gang. The next Monday, Ari finds out that Ileana dropped out of school because she got married after getting pregnant. 
In his next letter, Dante reveals that he is scared his parents will be disappointed in him if they find out that he wants to kiss boys.
On the last day of school, Ari asks Gina and Susie to drive him out to the desert so that he can get drunk.
Remember the Rain
The summer begins again and Ari begins to work full-time at the Charcoaler. Dante returns from Chicago and the two boys take Ari's truck to the desert. Dante reveals that his mother is pregnant. He hopes that the new baby will be a boy so that he can marry a woman and have children. While Ari has no problem with Dante's sexuality and will stand by him, he makes it clear he doesn't want Dante trying to kiss him either. 
One night, Dante convinces Ari to kiss him, saying it is an experiment as he has never kissed another boy and wants to know if he feels anything from kissing Ari. While reluctant, Ari agrees and Dante kisses him with Ari briefly kissing him back. Afterwards, Ari claims to have felt nothing while Dante is upset as he felt something with the kiss, seeming to confirm Dante has feelings for Ari. Following this event, it becomes increasingly clear that Dante is in love with Ari who appears not to reciprocate Dante's feelings for him.
Ari's mother goes to Tucson to visit his Aunt Ophelia leaving Ari and his father alone for a few days. Gina and Susie stop by the drugstore where Dante works, where he tells them about how Ari saved his life. Ari is furious that Dante broke their rule of not speaking about the accident.
Dante brings along two joints the next time he and Ari drive out to the desert and the two of them get high. Dante tells Ari that he likes a boy with whom he works named Daniel. It starts raining while they are in the truck. Both boys take off their clothes and run naked in the rain.
The next morning, Ari's father announces that Aunt Ophelia had had a fatal stroke. The two of them drive to Tucson. Ari remembers staying with his aunt for several months when he was younger. He asks his father why he was left to live with his aunt, and his father tells him that during Bernardo's trial, Ari's mother had a mental breakdown. Ari had to be sent away so that his Aunt Ophelia could take care of him.
At the funeral, Ari realizes that none of his extended family is there. He is told that they disapproved of Aunt Ophelia having lived with another woman for many years. Ari's own parents are angry that she was estranged from the rest of the family because of her sexual orientation.
After the funeral, Ari's mother offers to finally tell him all about Bernardo.
All the Secrets of the Universe
Ari's mother explains that Bernardo was arrested for murder. When he was fifteen years old, he hired a prostitute off of the street. The prostitute was transgender, whom an infuriated Bernardo killed with his bare fists. He is in prison for life.
When Ari returns home, Mr. Quintana tells him that Dante is in the hospital. He was jumped by several young men who had seen him kissing Daniel in an alley.
Ari goes to Dante's work and confronts Daniel, finding out the names of two of the men who attacked Dante. Ari visits one of them, Julian, at the body shop where he works and starts a fight with him.
Ari nearly ends up in trouble for what happened, but his father stands by him when he explains and Ari avoids having to pay Julian's hospital bills. His mother, who was afraid of Ari ending up like his brother, seems to gain an understanding of something that Ari misses after he explains how he beat up Julian because of his anger towards him for attacking Dante over kissing another boy.
After the attack, Mr. Quintana asks if Ari knows why Dante was jumped. Ari tells him that Dante is gay and was kissing another boy. He also explains that Dante hadn't told his parents out of fear of their reactions, but Mr. Quintana is supportive of his son along with his wife. Mr. Quintana admits that he'd guessed the truth because of the way Dante looks at Ari, while Mrs. Quintana tells Ari she thinks Dante is in love with him. Ari admits that's true, but believes that Dante has moved onto Daniel. Mrs. Quintana shares her belief that Daniel is just a stand-in for Ari.
When Dante comes home from the hospital, Daniel starts visiting him in his house. This angers Ari because Daniel ran away while Dante was being beaten up. Dante admits to Ari that when he kisses Daniel, he imagines he's Ari, but Ari just tells Dante he needs to get a new head. Dante is left upset by Ari's reaction to Dante all but admitting his love for him.
Ari's mother eventually calls a family meeting where she gets Ari's father to finally tell him about an incident in the Vietnam War that has haunted him. Ari's father tells him it's time they both stopped running, saying that Dante loves Ari. Ari is aware of this but thinks Dante has gotten over it. Ari's father explains that what Ari's running from, what will kill him if he keeps running, is that Ari loves Dante too. When Ari denies it, his father tells Ari that his instincts in saving Dante's life while risking his own and taking revenge on Julian point to Ari loving Dante more than he can bear. After his father's explanation, Ari finally accepts this, and breaks down, ashamed of loving another boy. However, his parents support him and his mother uses his Aunt Ophelia as an example. Ari's father reminds Ari of how when things got tough when Julian and his friends attacked him, Dante didn't run. In that moment, Ari and his father finally reach an understanding of each other.
That night, Ari, Dante and their parents go bowling together. Having accepted that he loves Dante, Ari is now a lot happier, especially when Dante reveals he realized Ari was right about Daniel. After bowling, Dante and Ari go out into the desert, where Dante tells Ari he can't be friends with Ari anymore because it's too hard for him to be friends with Ari when Dante loves him and Ari doesn't love him back. Rather than running from his feelings, Ari reminds Dante of their kiss and how he said it didn't work for him before finally admitting he lied about it. Ari asks Dante to kiss him again but Dante refuses, challenging Ari to kiss him instead. Without hesitation, Ari kisses Dante, fully accepting his love for him.
Following the kiss, Dante and Ari relax in the back of Ari's truck. Ari reflects that he'd been searching for the secrets of the universe and his own body and heart when the answers were with him the whole time in the form of his love for Dante. Ari now knows that he'd been in love with Dante from the moment they met, but didn't let himself know, think or feel it. Now free of his fears, Ari is left wondering why he was ever ashamed of loving Dante Quintana.