It is 1975; Joseph “Patch” Macauley is a thirteen-year-old boy born with one eye who intervenes in the attempted abduction of Misty Meyer, a girl from school, and winds up getting taken himself. Saint, who lives with her grandmother Norma, is an amateur beekeeper and Patch’s best friend. Devastated by Patch’s disappearance, she decides to do her own investigating. Misty Meyer tells Saint that she saw the town doctor, Dr. Tooms, at the scene of the crime in the woods. A few days later, news breaks out that a girl from a neighboring town, Callie Montrose, has gone missing. Saint sneaks out to investigate Tooms, and finds him at his house with blood on his hands—Chief Nix, the chief of the Monta Clare Police Department, dismisses the incident.

A boy from church, Jimmy Walters, shows romantic interest in Saint, but she cares only for Patch and is determined to bring him home. She tracks down a photographer she believes to be Patch’s captor, and finds his address. After telling Jimmy Walters what she intends to do, Saint goes there alone with her grandfather’s gun and asks the man, Eli Aaron, to photograph her. He admits to taking the girls, and Saint suddenly realizes she is in grave danger. As she is trying to escape, a fire is set in the house. Saint narrowly makes it out, rescued by Chief Nix. She runs into the woods and finds Patch, who is barely alive. Eli Aaron escapes.

The narrative then recounts Patch’s time in Eli Aaron’s bunker, where it is pitch-black and cold. A girl, Grace, comes to visit him; she tells him stories, and describes her home. She comforts him and gives him faith, becoming his lifeline during his imprisonment. When Saint comes to find him and the house begins to burn, Grace drags Patch out, saving his life. It is revealed that Eli Aaron has been hunting down and killing a number of young girls, burying them with rosary beads. 

When Patch is rescued, all he wants to do is find Grace. Misty Meyer tries to befriend him after what he did for her, but he can only focus on Grace. With his mother drunk and incapacitated most of the time, Patch takes up her old night cleaning job. Here he meets Sammy, the owner of Monta Clare Fine Art, who sets him up in a studio and tells him to start painting as a way to cope with his trauma. Patch starts painting portraits of Grace, despite not knowing what she looks like. Misty Meyer invites Patch to her birthday party, and Jimmy continues to pursue Saint, who is preoccupied with her own search for Grace. 

In 1978, Patch and Misty are dating. He is still searching for Grace, meeting the parents of other missing girls and painting portraits of their daughters. Saint gets into Dartmouth and agrees to go to prom with Jimmy Walters. On the night of prom, she sneaks onto Tooms’s property only to be caught by Chief Nix. She runs from him and discovers a bunker nearby that is covered in Callie Montrose’s blood. That same night, Patch breaks up with Misty so that she will go to college rather than stay in Monta Clare to be with him.

In 1982, Saint is training to be a cop under Chief Nix. Tooms is sentenced to death row for the murder of Callie Montrose, though he pleads not guilty. Patch’s mother dies, and Patch leaves Monta Clare, seeking out more missing girls and painting their portraits, then sending the paintings to Sammy to display in the gallery. He starts robbing banks and giving most of the money to missing persons charities.

Saint marries Jimmy Walters at Norma’s encouragement. She gets an offer to work with the FBI in Kansas City and takes it despite Jimmy’s protests, agreeing to help track down Patch. Patch calls her some time later and learns that Saint is pregnant; she traces his call and nearly catches him during a robbery. Patch, meanwhile, gets work on a fishing boat in New England. One night he goes to Boston and runs into Misty, and the two of them spend the night together and have sex.

Saint goes to a clinic, intending to get an abortion. She returns home to tell Jimmy, but before she can even finish her sentence he begins to beat her. That night she leaves Monta Clare and goes back to Kansas, where she pieces together Patch’s plot to visit all the places Grace once told him about. Using this information, she tracks him down and finally arrests him.

In 1990, Saint picks Patch up from his six-year prison sentence; she is now chief of the Monta Clare Police Department. One day Patch sees Misty Meyer on Main Street and they strike up a friendship. He finds out later that Misty has a daughter named Charlotte—his daughter. They decide not to tell Charlotte that Patch is her father, but he starts spending more time with them, committed to proving himself. He tears down his mother’s old house and builds a new one. 

Saint has been working on the Eli Aaron case as the remains of more missing girls are dug up, all found buried with a specific type of rosary bead. In 1993, Misty gets cancer and dies, leaving Charlotte in Patch’s care. By 1995, Patch has slowed his search for Grace and devoted himself to caring for Charlotte, helped by Sammy and Mrs. Meyer. They go together to New York City, where Patch’s paintings are being displayed in an art show that gets written about in the New York Times

Saint discovers that the rosary beads are from a church in a town called Black Rock, where the nuns recognize a photograph of Eli Aaron. He’s bought beads from them recently, proving to Saint that he is still on the hunt.

On Charlotte’s thirteenth birthday, Patch faints at the local zoo. He wakes up and finds he is being tended to by Jimmy Walters, the zoo’s vet, whom Saint divorced after he beat her. Patch knows of this, and punches Jimmy, who hits his head and dies. Patch is tried for murder, and sent back to prison. By 1998, he is working in the prison library, where he lobbies to give out books to the men on death row. His wish is granted, and he gets time every week to speak with Tooms, who is soon to be executed, in an effort to find out where Grace is. 

Saint takes over parenting Charlotte in Patch’s absence, and during that time Norma dies of a heart attack. After the funeral, Saint gets a call from the nuns in Black Rock, informing her that Eli Aaron just bought more beads and is heading to Florida. Saint and the FBI nearly catch him, arriving in time to save the girl he was after. 

Saint and Charlotte discover the skeleton of a dog on their property, and a moment later Saint is told that Callie Montrose’s father Richie has been killed; she finds from security camera footage that proves Nix is the killer. She goes to arrest him, but he shoots himself. 

While listening to old tapes from Patch’s rescue, Saint realizes that the dog bones on her property belonged to the dog Dr. Tooms always claimed to have been looking for the day that Patch was captured, proving his alibi. 

Patch is attacked in prison, and beats the guys up before being sent to solitary confinement. While there, he figures out during a conversation with another prisoner that Grace’s hometown is Grace Falls, Alabama. One night, helped by a number of people at the prison, Patch escapes. 

Saint finds a letter addressed to her in Nix’s house that exposes Tooms’s innocence. She frees him within the hour that he is slated for death, and he tells her everything: that he was providing abortions for young women, and during her procedure, Callie Montrose hemorrhaged and died. She’d been raped and impregnated by her father, Richie Montrose. Saint realizes that Eli Aaron is hunting down “sinners”—for instance, girls who have had an abortion or support abortion rights.

Patch arrives at Grace Falls, Alabama, and finds Grace’s old house. In a barn nearby, he finds Grace herself, who tells him to leave though she is overjoyed to see him; he discovers that Eli Aaron is her father. Saint traces a call that Patch had placed to Charlotte upon his arrival, and finds the house soon after Patch. There, she is attacked by Eli Aaron. He nearly kills her, but Patch shoots and kills him first. Saint lets Patch escape before the FBI arrives. 

In 2001, Patch has evaded arrest and is nowhere to be found. Charlotte is set to go off to college in Boston in a few weeks, and it is revealed that Saint never did get an abortion; rather, she had the child and gave him to another family to take care of. One day Saint and Charlotte receive a package of purple honey from North Carolina from Patch, and go on a road trip to search for him. They find him living on a boat in Outer Banks, North Carolina, where he spends his days sailing, painting, and reading letters from Grace. Patch gives Saint his latest painting: a picture of the two of them when they were children.