In the prologue, we meet a man named Elwood Curtis who is living in New York City. As a teenager, he attended the Nickel Academy, a reform school in Florida that is now being demolished. He reads in the newspaper that a secret graveyard has been discovered on the grounds and realizes that he needs to return to the school and tell his story.

Part One of the book takes place in 1962 in Tallahassee, Florida, where a teenage Elwood Curtis receives a record album of speeches by Martin Luther King, Jr. The speeches introduce him to the Civil Rights Movement and have a profound impact on his thinking. Since his parents left town, Elwood has been raised by his strict grandmother, Harriet. After school, Elwood goes to the Richmond Hotel where Harriet works, and he waits in the kitchen, interacting with the staff. One day the kitchen staff trick Elwood into a dish-drying competition and his prize is a set of encyclopedias left behind by a traveling salesman. After hauling the heavy books home, he discovers that all but one of the volumes are blank. Elwood is hurt that the staff took advantage of his trusting nature, and he stops going to the hotel. 

Elwood gets a job as a stock boy at Marconi’s Tobacco & Cigars, a neighborhood grocery. He reads magazines there and becomes more immersed in the Civil Rights Movement. He is smart and capable, but his grandmother and Mr. Marconi worry that his high ideals will get him in trouble. When he exposes some boys who are shoplifting candy, Mr. Marconi disapproves and the boys beat up Elwood after work. A teacher, Mr. Hill, arrives at Elwood’s high school and encourages Elwood’s enthusiasm for civil rights. He gives Elwood books to read, meets him at a local demonstration, and ultimately arranges for Elwood to take a class at a nearby community college. Elwood hitchhikes to see the school, and it turns out that the man who is giving him a ride is driving a stolen car. They’re pulled over by the police and Elwood gets arrested. 

At the beginning of Part Two, a judge sentences Elwood to a reform school called Nickel Academy. He’s taken there in handcuffs with two white boys. Once they arrive, Elwood is hopeful because the Academy looks like a school, not a prison. He is assigned to Cleveland dormitory on the Black students’ campus. The next morning, Desmond, a boy from his dormitory, shows him around. Elwood learns that Nickel is not providing an education, and he is assigned to work on the yard crew with Jaimie, a Hispanic boy who is moved back and forth from the Black campus to the white campus. Desmond and others tell Elwood how to get along at Nickel so he can get released early. Elwood vows to keep quiet and get out early. However, when he sees a boy, Corey, being bullied in the bathroom, he steps in to intervene. All four boys, including Corey and Elwood, are taken from their beds in the middle of the night by the superintendent, Maynard Spencer, and a white houseman named Earl, and subjected to a brutal beating in a building called the White House.

Elwood wakes up from the beating in the school infirmary, where he stays for two weeks until his legs and back have healed. Turner, Elwood’s best friend, eats soap powder to make himself sick so he can visit Elwood. Turner counsels Elwood to try to avoid conflict. Elwood, however, believes that if people are confronted by injustice, they will do the right thing. However, when he sees the scars on his legs from the beating, Elwood is ashamed that he let himself be beaten so badly and doesn’t tell his grandmother about the incident when she visits. 

When Elwood returns to Nickel campus life, Turner gets him a new job called “Community Service.”  Elwood and Turner leave campus in a van with a white 20-year-old named Harper. They bring goods that meant to be used for the Black boys at Nickel and distribute them to local businessmen. The businessmen give envelopes of money to Harper for the medicine, food, and other supplies. Harper then gives the money to Superintendent Spencer and his boss, Director Hardee. After this, Harper leaves Turner and Elwood at the home of one of the board members to paint his gazebo. At night, Elwood writes down everything they do in a notebook.

Every year at Nickel there is a student boxing match between the best Black boxer and the best white boxer. This year the Black boxer is a large, violent bully nicknamed Griff. Superintendent Spencer tells Griff that he needs to lose the fight on purpose, pretending to be knocked out in the third, final round. But the night of the fight, Griff wins. He tells Spencer that he lost track of the rounds and thought there was one more. That night, Spencer and Earl take Griff “out back,” chain him between two trees, and beat him to death. The boys on campus convince themselves that Griff escaped, but his body is found in the secret cemetery decades later.

The students work on an elaborate Christmas Festival containing lights and large displays that attract paying tourists. The festival includes a staff luncheon, and Jaimie puts poison in housemaster Earl’s drink, hoping to kill him. But Earl lives and no one realizes he was poisoned. 

Part Three of the book alternates between adult Elwood’s life in the 1970s and teenage Elwood’s life in Nickel. In the 1970s, Elwood has a girlfriend and is working for a moving company in New York City. He buys his own van and starts a company, Ace Moving, which he later realizes he named after the highest level of achievement at Nickel. 

Back in the 1960s, Elwood realizes that Nickel is breaking him down. The merit and punishment system at Nickel is arbitrary and he feels unable to earn early release. He is losing hope and losing his belief in the teachings of Martin Luther King, Jr. When his grandmother tells him that the lawyer she hired to help him left town with their money, Elwood decides he wants to expose Nickel’s injustices and get the school closed down. 

In the 1980s, Elwood, now the owner of a successful moving company, is recognized on the street by Chickie Pete, who was a fellow student at Nickel. They go to a bar for a drink, and Elwood reflects on how damaged all the boys from Nickel are. Chickie Pete has just gotten out of rehab and has no job or place to live. Elwood is a successful businessman, but he struggles with relationships and is still unmarried. Chickie Pete asks Elwood for a job, but Elwood throws Chickie Pete’s contact information out the window on his cab ride home.

In the 1960s, Spencer is told about an upcoming “surprise” inspection by the state, and all the boys get busy fixing up Nickel and hiding its secrets. Elwood decides to give his notebook, which details the corruption at Nickel, to one of the inspectors. Turner tells him that this is a bad idea and begs him not to do it. Elwood again states his philosophy that people are ultimately good and want to do what is right. On the day of the inspection, Elwood is sent on an errand and is unable to give his notebook to the inspectors, so Turner volunteers to do it for him. When they meet up again, Turner tells Elwood that he handed the notebook to an inspector who looked like John F. Kennedy through the car window as he was leaving. A few nights later, Spencer and his new assistant, Hennepin, come for Elwood at night and he is beaten at the White House. 

In the 2000s, Elwood meets his wife Millie at a fancy restaurant in Harlem. He reflects on a time when the neighborhood was more run-down. 

When the narrative returns to the past, Elwood is locked in a dark room on the top floor of the dormitory, a form of solitary confinement that has been outlawed by the state. He’s there for weeks, subsisting on hardly any food and subjected to extra beatings by Spencer and Hennepin. One night, Turner comes and gets Elwood, telling him that the boys overheard that the following night Spencer is going to take him “out back” and kill him like they killed Griff. Turner and Elwood run away, taking bikes from a house they had cleared out as part of Community Service. They ride all night and through the next day, trying to get to Tallahassee. Turner and Elwood are almost there when a white van pulls up beside them—the Community Service van from Nickel. The boys run across a field as Hennepin and Harper shoot at them with rifles. Hennepin misses, but Harper shoots Elwood, who falls to his death with arms outstretched. Turner keeps running, leaving Elwood behind. 

Back in New York in 2014, Turner, who took Elwood’s identity after he escaped, tells his wife Millie the true story. He tells her about his time in Nickel and reveals his full name: Jack Turner (though no one but his mother has ever called him Jack). They cry together, and Millie commits to helping Turner heal from the trauma of his horrific experience.

The next day, Turner flies to Tallahassee to attend a hearing where the Nickel boys will tell the stories of the atrocities they witnessed and endured. Turner is the only Black alumnus testifying. Turner plans to tell the story of Elwood’s death, and presumably Griff’s story and other accounts. Before the hearing, he has lunch in the restaurant at the hotel where he is staying. The hotel is now called the Radisson, but it used to be the Richmond Hotel. Although Turner doesn’t make the connection, this is the same hotel restaurant where young Elwood sat in the kitchen waiting for his grandmother and dreaming of the day that a Black man would be served in the dining room.