The novel follows fifteen-year-old Mickey Bolitar as he adjusts to life in Kasselton, New Jersey, after his father's death in a car crash and his mother Kitty's descent into addiction. Mickey lives reluctantly in the basement of his uncle Myron Bolitar's house, the same home where Myron and Mickey's father, Brad, grew up. Myron, a former first-round professional basketball draft pick turned sports agent, took Mickey in after Brad died, but the two share a strained relationship rooted in Myron's cruel accusations against Kitty years earlier when she became pregnant at seventeen.
Walking to school one morning, Mickey encounters the Bat Lady, a reclusive, seemingly ancient woman who lives in a dilapidated house long rumored by local children to be the home of someone who kidnaps those who pass after dark. She calls Mickey by name and tells him his father is "very much alive." Mickey knows this cannot be true because he witnessed his father die, but the words unsettle him deeply.
At school, Mickey has two bright spots. The first is Ema, a goth-styled freshman whom he defended during a humiliating team-building exercise at orientation. The second is Ashley Kent, a preppy new sophomore with whom Mickey develops a tentative romance over three weeks. Ashley suddenly stops coming to school. Mickey cannot reach her by phone, has no home address for her, and finds nothing about her online. His teacher Mrs. Friedman reveals she received a note saying Ashley would not return.
Mickey begins investigating on two fronts. He returns to Bat Lady's house with Ema and discovers a hidden garage behind it. They break in through the decaying back door, finding a living room frozen in time: a turntable with an album by HorsePower, a band his mother once knew, and a photograph of five hippies from the 1960s wearing T-shirts bearing a strange butterfly emblem. A black car with tinted windows arrives at the garage, and a bald man in a dark suit emerges. Ema distracts him while Mickey hides, then records the car's license plate: A30432. The bald man later appears near Myron's house and tells Mickey, "You have questions, but you're not yet ready for the answers" (111), warning him to tell no one.
Meanwhile, Mickey enlists Spoon, a quirky student whose father is the school janitor, to access Ashley's student file. They find her listed address on Carmenta Terrace. When they arrive, police surround the house: Dr. Kent, Ashley's supposed father, has been assaulted in a home invasion, and Mrs. Kent says the intruder had a tattoo on his face. When Mickey asks about Ashley, Mrs. Kent replies that she has no daughter and does not know anyone by that name.
Mickey's home life fractures further when Kitty is released from rehab seemingly healthy but relapses the same day. Mickey and Myron track her to a squalid motel, where they find her passed out and high. They return her to rehab, and the director bars all visitors for at least three weeks.
The investigation deepens when Mickey and his family fly to Los Angeles to visit Brad's grave. On the temporary placard, Mickey notices the same butterfly emblem from Bat Lady's photograph. Back in New Jersey, Spoon retrieves surveillance footage showing a man with a face tattoo breaking into Ashley's locker. Ema takes a still image to Agent, a tattoo artist, who identifies the man as Antoine LeMaire and provides an address: the Plan B Go-Go Lounge in Newark.
Using a fake ID, Mickey enters the Plan B, a seedy go-go bar. He is dragged to a back office where he meets Buddy Ray, the club's owner, who punches him and demands to know where Ashley is. Mickey escapes by head-butting a bouncer named Derrick and creating chaos onstage. A dancer named Candy helps him flee through a fire exit, revealing that Ashley was her only friend and that Antoine "got her months ago," though Candy is confused when Mickey says Ashley was recently at his school.
A breakthrough comes when Spoon discovers that Rachel Caldwell, the most popular girl in school, used Ashley's locker combination to clean it out before the intruder arrived. Mickey confronts Rachel, who reveals that she witnessed a large man try to force Ashley into a car. Rachel intervened, and Ashley confided that her real last name was not Kent. Ashley had assumed the identity of a childless Kasselton family to enroll in school after escaping a nightclub where she was being sexually exploited. Rachel hid Ashley in her family's pool house, but Ashley has since fled, leaving a note saying she cannot hide forever. Rachel discovers that Ashley received an email from Candy pleading for help, claiming Buddy Ray was punishing Candy for helping Ashley escape.
Late at night, Mickey and Ema find a tombstone behind Bat Lady's garage inscribed with the initials "E.S.," the phrase "A childhood lost for children," the number A30432, and the butterfly emblem. Ema's research connects these to Lizzy Sobek, a thirteen-year-old Polish Jewish girl who escaped Auschwitz and rescued hundreds of children during the Holocaust, known as "the Butterfly." Mickey also learns that the species depicted in the emblem is named after Abeona, the Roman goddess who protects children on their first journey from home, linking it to the Abeona Shelter, the charitable organization for which Mickey's parents worked. Ema reveals she has the same butterfly emblem tattooed on her back, deepening the mystery.
When Mickey attempts to re-enter Bat Lady's house, the town's police chief arrests him for trespassing. As the cruiser pulls away, Mickey sees Bat Lady in her upstairs window, mouthing the words "Save Ashley."
Mickey, Rachel, and Ema return to the Plan B to rescue Ashley. Derrick ambushes Mickey outside at gunpoint, but Antoine LeMaire shoots Derrick dead and reveals his true identity. Antoine's criminal persona is a cover; he works for the Abeona Shelter, rescuing girls from Buddy Ray's trafficking operation. He explains that Ashley's mother died working for Buddy Ray, who claimed Ashley owed her mother's debts. The shelter rescued Ashley and placed her under a new identity in Kasselton, but a newspaper photo from school orientation allowed Buddy Ray to track her down. Antoine cannot blow his cover, so Mickey must save Ashley himself.
Inside the club, Rachel and Ema stall the staff while Mickey finds Ashley tied to a chair in the basement, threatened by Buddy Ray with a knife. Mickey frees her and tackles Buddy Ray. When Buddy Ray corners Ema with a knife to her throat, Spoon, whom Ema called for backup, crashes his father's truck into Buddy Ray, saving Ema's life. Police arrive, and Ashley gets into Antoine's van and drives away. Mickey senses they may never see each other again.
Days later, the bald man's black car brings Mickey through a tunnel into Bat Lady's house. She confirms she is Lizzy Sobek. She recounts her family's transport to Auschwitz, her father's escape with her into the woods, and the Butcher of Lodz, a Waffen-SS officer who lined escapees beside a pit and shot them. Her father pushed her in and shielded her with his body. She lay beneath his corpse all night before crawling out. She explains the Abeona Shelter's philosophy: They save who they can, making painful choices because overreaching risks everything.
Then she shows Mickey a photograph of the Butcher of Lodz in his uniform. Mickey recognizes the man, not as an aged Nazi, but as the sandy-haired, green-eyed paramedic who took his father away in the ambulance after the car crash, looking exactly the same age as in the seventy-year-old photograph. The novel ends on this revelation, with Mickey's understanding of his father's death fundamentally shattered.