The novel alternates between two perspectives. In chapters labeled "Below," an unnamed captive is chained in an underground bunker, where the door has not opened in days. She hallucinates ghostly figures she calls "gossamer girls," conjured from names and survival instructions carved into her bed frame by previous captives: Amanda, Madison, and others. With her food and water nearly gone, she resolves to break her chain and escape.
In chapters labeled "Above," Audrey Dixon, a school counselor and Search and Rescue volunteer in Franklin, joins the search for a missing four-year-old named Bryson Lee. Audrey's dedication stems from guilt over her best friend Janie Martin, who disappeared years ago without Audrey noticing. During the search, Audrey crosses onto private land belonging to Terry Butler and discovers "witch beads," white beads on a string associated with a local folktale about Jenny Red-Hands, a vengeful spirit said to avenge wronged girls. The beads remind Audrey of Janie, who left an identical set on Audrey's windowsill the last night she appeared, and of Meghan Vale, a Franklin High student who vanished three months earlier. Bill Butler, Terry's brother, confronts Audrey at gunpoint for trespassing, but Emily Hill, the youngest sibling of the prominent Hill family, defuses the situation. Bryson is found alive shortly after.
Emily is a reclusive painter who lives on the adjacent Hill property. Her older siblings are Melinda, who runs a shelter called Hope's Hands and harbors political ambitions; Andrew, a former football player; and Liam, an actor. Audrey investigates Meghan's disappearance and discovers that Meghan posted a photograph of a tree draped in witch beads to her private Instagram two weeks before she vanished, with a caption suggesting someone was watching her. In an episode of a true crime podcast, Meghan declared she had seen Jenny Red-Hands in the woods. Audrey grows convinced that Meghan's disappearance connects to whatever is happening on the Butlers' and Hills' land.
In the bunker, the captive fashions a makeshift wrench from aluminum chair legs and uses it to remove bolts from the toilet base. She works one bolt against a weakened chain link, trying to pry it apart. Despite dwindling supplies and failing flashlight batteries, she persists, driven by the knowledge that if the door never opens again, she has nothing to lose.
Audrey visits Meghan's hostile father and secretly takes a diary from under Meghan's bed. In it, Meghan describes seeing a ghostly woman with pale hair and hands dipped in blood moving through the woods. The diary's final poem ends with the line "My name is Stranger," echoing words carved in the bunker. Audrey confronts Emily, who admits she met Meghan but insists the conversation was private. Emily urges Audrey to stop looking. Audrey also learns from Bill that Andrew, not Terry, has been tending Terry's land, contradicting what Emily implied.
Meanwhile, Audrey begins dating Dev Khanna, a social studies teacher at her school. Dev becomes her partner in the investigation when they return to the woods at night with Barry, Audrey's pit bull-mastiff mix. Barry alerts to buried remains in a clearing and leads them to a hidden metal door set into a hillside. Inside, they find a concrete bunker with a chain on the wall, red handprints covering the surfaces, and names carved into broken bed slats. Barry alerts again, signaling the scent of death. Audrey matches the names to real missing persons cases involving young women with red or auburn hair who resembled Janie.
Part II reveals the bunker's original discovery. After their father Mason Hill's death, the four Hill siblings find the captive, referred to as Stranger, alive in the bunker. She has been chained there for months, one in a line of young women Mason abducted and murdered. The siblings debate calling the police. Melinda hesitates, calculating the damage to their reputations. Andrew argues against reporting it. Stranger, drawing on knowledge of the siblings gleaned from months of Mason talking about his children, manipulates each of them to survive: making herself small for the volatile Andrew, appealing to Melinda's pragmatism, and cultivating Liam's guilt.
Audrey and Dev report the bunker to Len Howard, Audrey's closest friend and a local deputy, who arranges a meeting with Chief Wagner. Wagner dismisses the evidence and refuses to investigate, citing the Hills as a respected family. Audrey and Dev return to the woods and unearth a skull. They are arrested but released when Melinda intervenes. The FBI takes over, eventually finding five bodies. Hair trophies in Terry Butler's attic bolster the official narrative naming Butler as the sole killer. Emily tells Audrey this outcome was inevitable: The Hills will express horror, blame Butler, and Melinda will emerge as a champion for victims.
The past timeline reveals Stranger's escape from the Hill house. Emily, herself kept isolated by Mason from age 14, discovered her father's crimes and eventually assisted him. She leaves Stranger's bedroom door unlocked and provides running shoes, but waits outside with a hammer. She attacks Stranger, who fights back and kills Emily in self-defense. Melinda arrives and reveals she discovered Mason's crimes weeks earlier, poisoned him with Terry Butler's heart medication, and had been arranging new identity documents for Stranger. Melinda claims responsibility for Emily's death and proposes a solution: Stranger will assume Emily's identity. Liam stages a car accident to justify reconstructive surgery on Stranger's face, and the family buries the real Emily in the woods.
In the present, Liam calls Audrey from Los Angeles, intoxicated and possibly overdosing, speaking incoherently about guilt. Audrey races to the studio of the woman she knows as Emily, where she finds dozens of portraits of red-haired girls labeled with the victims' names and a back room replicating the bunker. The real Emily Hill's diary sits on a bed inside; Stranger has studied it to inhabit Emily's identity. Stranger confirms the bunker was not empty when the siblings found it. Melinda arrives with a gun and reveals Liam has died of an overdose.
Stranger explains that she met Meghan Vale, who discovered the truth, and helped Meghan disappear with a new identity. But Meghan returned, enraged by the public lie blaming Terry Butler. Melinda reveals that Liam learned Meghan had returned and that Andrew now knew as well. Melinda forces Audrey at gunpoint to drive to a remote cabin, where they find Andrew holding Meghan at gunpoint. He proposes killing all witnesses. Melinda steps in front of the gun to protect Stranger, and Andrew shoots her. Meghan flees. Andrew pins Audrey down and begins strangling her, but Barry, who broke through the car window, attacks him. Stranger takes the gun and kills Andrew.
Stranger and Meghan vanish together using identity documents Melinda had prepared. Before leaving, Stranger tells Audrey there is another cage waiting if she stays. In the days that follow, Audrey recovers at the home of Len and his partner, Kenny. When Dev returns, Audrey tells him the persistent hum that drove her search for years has finally gone quiet.
In the epilogue, Stranger, now living under a new name with Meghan, addresses Audrey directly. She confirms she is Janie Martin. She explains that the night she came to Audrey's window years ago, she realized her face, reshaped by deprivation and surgery, was no longer recognizable. She closes: "You'll be okay, Oddity. And so will I."