In the late spring of 1976, fifteen-year-old Boady Sanden lives with his widowed mother, Emma, on Frog Hollow Road, a dead-end gravel road in rural Jessup, Missouri. Boady is a lonely, friendless freshman at St. Ignatius Catholic High School. His father, John, died falling from scaffolding when Boady was five, and Emma has been consumed by grief ever since, a state Boady calls "the sadness." He secretly plans to run away at sixteen, saving money from his drywall job.
At school, Boady learns about the disappearance of Lida Poe, a Black woman who worked at Ryke Manufacturing, the town's largest employer. He overhears Jarvis Halcomb, a popular senior and son of Ryke's manager Cecil Halcomb, mention that a Black investigator is coming from Minneapolis to examine embezzlement. When Jarvis proposes dumping pudding on Diana Jackson, the only Black student at St. Ignatius, Boady trips the boy carrying it and flees to the cafeteria kitchen, where a worker hides him.
Boady's neighbor Hoke Gardner, a quiet man in his sixties with an injured left arm and burn scars, tells Boady the long-vacant house across the street has been sold to a family named Elgin with a son his age. Hoke writes constantly in black notebooks with red spines but reveals nothing about his past. When Sheriff Matthew Vaughan visits, Boady eavesdrops and learns that Poe once worked for Hoke in Columbia, Missouri, and that Hoke's wife died in a suspicious accident. The sheriff hints at fraud before Hoke orders him away.
The local paper reports that Cecil has been demoted after evidence of embezzlement surfaced, and Charles Elgin is arriving from Minneapolis to take over operations. When Boady asks if the family is Black, Hoke challenges his claim of holding no prejudice. At school, Jarvis reveals his connection to the CORPS (Crusaders Of Racial Purity and Strength), a local white supremacist group. He pressures Boady to spy on the Elgins and later orders him to vandalize their house, threatening Emma by name. Boady refuses, and Jarvis retaliates with escalating violence through the final days of school.
Boady's first meeting with Thomas Elgin goes badly when he uses a racial slur in a casual expression. Thomas walks away, and Hoke explains that the word carries the weight of history. After a difficult week, the boys reconcile; Thomas confides his resentment at being uprooted from Edina, Minnesota, and his dream of becoming an actor. Thomas's mother, Jenna, sparks a bond with Emma that draws Emma out of her isolation. Emma begins spending Saturday mornings on the Elgins' porch, talking and laughing more than Boady has ever seen.
That summer, Boady and Thomas work together at the drywall company. On a camping trip, they discover an abandoned church serving as CORPS headquarters, with shooting targets, Confederate flags, and recruitment flyers. Nearby, Boady's coonhound Grover uncovers a human hand beneath a fallen log. Boady identifies faint tire tracks with a distinctive missing chunk of tread. They report the find, but Vaughan dismisses Boady's observations, and deputies destroy the prints by driving over them. When Boady returns to the burial site, he sees Lida Poe's face and a bullet hole centered between her eyes.
Charles fires Cecil from Ryke, deepening the town's racial divisions. Days later, two masked men attack Boady and Thomas from a pickup truck. Thomas spots a tire print identical to the tread near Poe's grave, linking the attackers to her murder. Boady's boss, Wally Schenicker, realizes only he and Milo Halcomb, Cecil's brother, knew the boys' location and fires Milo, who retaliates by exposing Wally's same-sex relationship. Hoke exposes Vaughan's conflict of interest as Cecil's second cousin. The boys lead investigators to Poe's missing car in a ravine, where they find Milo's lighter. Detective Dillon Royce is assigned to assist, and Milo is arrested.
Boady and Thomas research Hoke's past at a newspaper archive and learn that in 1966, Hoke, then a criminal defense lawyer, drove off the road and hit a tree. The car caught fire, killing his wife, Alicia, and their five-year-old daughter, Sarah. At a Fourth of July dance, Boady dances with Diana, who thanks him for the pudding rescue with a kiss. Hoke later tells Boady the story of Emmett Till, a fourteen-year-old Black boy murdered in Mississippi in 1955, and argues that prejudice cannot be erased by laws alone.
One night, a cross is burned on the Elgins' lawn, and a rock hurled from a speeding truck fractures Emma's skull, causing a coma. Wally's house is also set on fire. While Emma is hospitalized, Boady stays at Hoke's house and discovers a locked trunk containing ten volumes of notebooks. They form a single letter to Mariam Fisk, Hoke's sister-in-law, beginning: "I am writing this letter to explain why I haven't yet killed myself" (218). Boady reads that months after the accident, Hoke attempted suicide at his family's graves, but the gun misfired repeatedly, grazing his skull. He stumbled to a church rectory and was taken to a hospital, where a doctor told a young woman her husband, John, had died. A little boy wandered over and said his name was Boady. That encounter gave Hoke a reason to live. He moved to Frog Hollow Road and spent a decade supporting them in secret, buying Boady a dog and paying for his schooling through a fabricated scholarship.
Emma recovers, and the investigation closes when Milo's credit card is traced to Texas. Events turn violent when Boady and Thomas sneak to a drive-in movie and Jarvis spots them. In the chase, Thomas leaps off a bluff into a cedar tree, and Boady follows. Jarvis attempts the same jump headfirst and breaks his neck. Boady recalls Jarvis tapping between his own eyes at the bluff, claiming a bullet there was not as clean and that he knew this for a fact. The boys theorize that Jarvis killed Poe as a CORPS initiation orchestrated by Cecil.
At the Elgin house, Cecil, Bob Decker, one of Jarvis's close friends, and Angus, Milo's son and Jarvis's cousin, are waiting. Cecil orders Angus to kill the boys. Boady stabs Bob with his father's pocketknife and breaks free, but Cecil shoots him under the collarbone. When Angus raises the gun, Boady pleads with him, and Angus lowers it. Hoke bursts through the front door with a revolver. In the exchange of gunfire, Cecil shoots Hoke three times. When Cecil aims at Boady, Hoke steps between them and takes the bullet. With his final shot, Hoke hits Cecil in the neck. Cecil flees, and Hoke dies in Boady's arms.
Bob's confession reveals the truth: Cecil used Poe as his accomplice and lover, then had Jarvis kill her to earn a CORPS tattoo. Milo helped stage alibis, but when he threatened to talk, Cecil murdered his own brother and buried him beneath a shed. Cecil's truck is found submerged in a river; he is presumed dead, though his body is never recovered.
In the aftermath, Boady reads Hoke's journals and persuades Emma to do the same. They ask Mariam Fisk for permission to bury Hoke with his family. Mariam refuses but arrives at Frog Hollow weeks later, having read the journals, and grants permission. Boady abandons his plan to run away, deciding to pursue college instead. At the burial in St. Peter Cemetery, Boady stands where Hoke once tried to end his life. When his turn comes to speak, he says only, "Thank you, Hoke." Emma, who has not sung since her husband's death, begins "Amazing Grace" as Jenna joins in harmony and Boady mouths the words.