Part One of Wonder is told from August “Auggie” Pullman’s point of view. Auggie was born with a genetic syndrome that gives him tiny ears, low eyes, and a misshapen mouth and jaw. By the time he is twelve, he has endured twenty-seven surgeries. Auggie lives in New York City with his parents, his sister, Olivia or “Via,” and his dog, Daisy, and until the novel begins, he has been homeschooled. 

Mom wants Auggie to go to middle school, but Dad feels hesitant, worried the other students will be cruel. Mom takes Auggie to meet Beecher Prep’s principal, Mr. Tushman, who has arranged for three other students—Jack, Charlotte, and Julian—to give Auggie a tour of the school. On the first day of school, Auggie faces a barrage of shocked reactions and surprised looks as people react to his appearance for the first time. Julian teases and provokes Auggie. Mr. Browne, their English teacher, gives his students a precept every month to think and write about. The first precept is about kindness. Auggie becomes good friends with Jack and a girl named Summer who sits with Auggie at lunch of her own volition. However, on Halloween, Auggie overhears Jack telling others that he wishes Auggie would stop following him around. Hurt and rejected, Auggie questions whether he should be in school at all.

Part Two is told from Via’s point of view. Since Auggie’s birth when she was four, she has had to be independent and take a back seat to Auggie’s needs. After Via returns from spending a few weeks with her grandmother, she sees Auggie as others see him for the first time. As Via enters high school, she feels estranged from her former best friends, Ella and Miranda. Miranda has also been a good friend to Auggie and gave him the astronaut helmet that he wore for several years. Auggie confides to Via what he overheard Jack say on Halloween, and they agree school is hard for everyone, but Via encourages Auggie to “suck it up.”

In Part Three, which is told from Summer’s point of view, Summer explains that she chooses to be Auggie’s friend despite criticism from other students. They work on an Egyptian Museum project at her house, where Auggie learns more about Summer’s personal life, including the fact that her father died. Auggie and Summer talk about death and agree that maybe people get to come back with new faces. They talk openly about Auggie’s appearance. When Jack later asks Summer why Auggie is upset with him, she gives him a hint but isn’t explicit.

Part Four is told by Jack. He recalls the day when he gave Auggie the tour of the school but also recalls having seen him outside an ice cream shop before. He is used to Auggie’s face and genuinely likes him as a friend. One day, Jack has an epiphany and finally understands what Summer’s hint meant and why Auggie has been upset with him. Jack feels guilty that he lied to others about his feelings about Auggie. When Julian calls Auggie a “freak,” Jack punches him in the mouth, but he will not tell Mr. Tushman why. Mr. Tushman sends Jack home until after winter break as punishment. Through Facebook messages, Jack apologizes to Auggie, and the boys are friends again. Julian’s mother tells Mr. Tushman that Auggie doesn’t belong at Beecher Prep, but Mr. Tushman disagrees. After the break, Charlotte describes the students who are on Julian’s side, on Auggie’s side, and neutral. Jack goes to Auggie’s house to work on a science fair project. He meets Via and realizes that she knows about what happened on Halloween. Via introduces Auggie and Jack to her boyfriend, Justin.

Part Five is told by Justin. Although he’s unsettled when he meets Auggie, he likes Via and her family very much, especially compared to his parents, who are divorced and rather absent. At school, Justin is cast as the lead in Our Town, and Via has a small part and serves as an understudy for Miranda, who has been cast as Emily, the female lead. When Justin witnesses Julian and others teasing Jack one day, he tells the boys to leave Jack alone. He learns that Miranda and Via were once close friends, and Via confesses that she hasn't told her parents about the play because she doesn’t want them to bring Auggie. She is ashamed that she feels embarrassed by her brother.

In Part Six, Auggie’s point of view returns. He cringes through the science fair because so many people react to seeing him for the first time. Julian puts mean notes in Auggie’s and Jack’s lockers, but Auggie notices that students are accepting him more. When Auggie gets hearing aids, life improves dramatically. However, when he learns that Via doesn’t want him to go to her play, he angrily explodes. Meanwhile, Daisy must be euthanized, which saddens the whole Pullman family, but ultimately draws them closer together and assuages the discord between Auggie and Via. Auggie attends Via’s play with his parents, and they are delighted when they see her playing the lead. Via and Justin get standing ovations.

Part Seven is told by Miranda. In the summer before high school, at camp, she lies and tells people that she has a brother with a deformed face, which increases her popularity. Miranda’s parents are divorced and distant, but she feels safe with Via’s loving family. However, Miranda changes that summer, both in appearance and in attitude. She is cast as the lead in Our Town, but on opening night, when she sees Auggie in the audience and realizes that no one has come to see her, she pretends to be sick so that Via can play the lead. After the play, Miranda sees Auggie backstage, and they hug. The Pullmans invite her to join them for dinner, and she happily accepts.

Part Eight returns to Auggie’s point of view. When his class, minus Julian, goes to the Broarwood Nature Retreat for three days, he feels both excited and afraid. He has a vision of Daisy on his first morning and enjoys nature walks and campfires and horseback riding. On movie night, when Jack has to use the bathroom, Auggie goes with him. In the woods, they meet a group of seventh graders who say awful things to Auggie. A fight breaks out. Jack and several other boys defend and protect Auggie. Auggie gets hurt and loses his hearing aids. 

When Mom picks him up the next day, Auggie says that he had a great time except for the last night. Dad brings home a new puppy. Back at school, Auggie has become a hero along with Jack and the other boys who defended him in the woods. Julian has become irrelevant, and Auggie learns that Julian won’t return to Beecher Prep the following year. When Dad drops Auggie off for his fifth-grade graduation, Dad admits that he is the one who threw away Auggie’s space helmet years ago. Auggie feels angry but forgives him. During the ceremony, Auggie wins the Henry Ward Beecher Award for his strength and kindness and receives a standing ovation. As the Pullmans walk home, Auggie thanks his mother for sending him to school, and his mother thanks him for being such a wonder.