FBI Special Agent Atlee Pine returns to her childhood hometown of Andersonville, Georgia, to investigate the nearly 30-year-old abduction of her twin sister, Mercy, only to become entangled in a series of present-day murders.
Pine, the sole FBI agent stationed in Shattered Rock, Arizona, near the Grand Canyon, has been visiting convicted serial killer Daniel James Tor at ADX Florence, the federal supermax prison in Colorado, believing he may have kidnapped Mercy from their shared bedroom in 1989. As a six-year-old, Pine witnessed an intruder use the nursery rhyme "Eeny, meeny, miny, moe" to choose between the twins, select Mercy, and fracture Pine's skull. Tor toys with Pine across three visits, questioning whether her hypnotherapy-recovered memory is reliable. On the drive home from one visit, Pine intercepts an Amber Alert and rescues a kidnapped girl but severely beats the abductor in an uncontrolled rage. Her superior, Clint Dobbs, the head of the FBI in Arizona, shields her from disciplinary action but warns she has used her one free pass and suggests she take time off to address her personal issues. Pine's assistant, Carol Blum, a veteran Bureau employee in her sixties, insists on accompanying her to Georgia.
Andersonville is a small town of about 250 people, known for the notorious Confederate prison where approximately 13,000 Union soldiers died during the Civil War and for the adjacent National Historic Site and cemetery. Pine and Blum visit her dilapidated childhood home, now occupied by Cyrus "Cy" Tanner, an amiable handyman in his sixties. They settle into a local bed-and-breakfast run by Lauren Graham, a woman who knew Pine's family. Over the next several days, Pine meets people from her past: Agnes Ridley, an elderly woman who babysat the twins; Sheriff Dave Bartles, who worked the original case as a deputy; and Jackson Lineberry, a wealthy investment manager who was close friends with her parents. Lineberry reveals that he discovered Tim Pine's body after Tim died by suicide, contradicting what Julia Pine had told her daughter. Pine also shares fragmentary details of her family history with Blum: Her father died by suicide on her 19th birthday, and her mother abandoned her during college, leaving only a brief note and enough money for her education.
Pine visits Myron and Britta Pringle, a couple who lived near the Pine family. Myron is a tall, eccentric computer genius who designs trading algorithms for Lineberry's firm; Britta is more conventional, preferring the Cape Cod-style guesthouse behind their contemporary home. Both their adult children died within a month of each other: Mary of a heroin overdose and Joe from a gunshot wound while cleaning his weapon. Myron is evasive about the night of Mercy's disappearance, and Pine senses both Pringles are withholding information.
The cold case yields a critical breakthrough when Pine revisits her childhood bedroom and realizes that a swivel mirror next to the window could have reflected the intruder's image. The man she saw likely entered through the interior door, not the window. This explains the absence of ladder marks outside and raises the disturbing possibility that the attacker knew the family and passed through the house.
A parallel crisis erupts when the body of a young woman wearing a vintage 1940s wedding veil is found posed on Andersonville's main street. Georgia Bureau of Investigation (GBI) Detective Max Wallis asks Pine to assist. The victim is identified as Hanna Rebane, an Estonian adult film actress from Columbus, Georgia. Rebane's roommate and fellow actress, Beth Clemmons, describes Rebane as recently secretive and influenced by someone new. Days later, a second victim, Layne Gillespie, a former soldier and drag performer from Savannah who also appeared in pornographic films, is found on a grave at the cemetery dressed in a vintage tuxedo. FBI Special Agent Eddie Laredo, with whom Pine has a complicated professional history from their time at the Bureau's Behavioral Analysis Unit, arrives to lead the federal investigation. He and Pine reconcile their past tensions and begin working together.
When Clemmons is found murdered in her apartment, Pine concludes she was killed to prevent her from connecting Rebane and Gillespie. A third staged victim, ten-year-old foster child Frankie Gomez, is discovered in the Drummer Boy Civil War Museum dressed in a Confederate drummer boy's uniform. A damaged St. Christopher's medal bearing gunshot damage and traces of someone else's blood hangs around his neck. Pine and Laredo theorize the killer is constructing a symbolic "nuclear family" of corpses: a bride, a groom, and now a child.
Myron Pringle reveals that Pine's mother was an international fashion model named Amanda who walked runways in London as a teenager, and that Tim Pine had aspired to be an actor in New York. Pine discovers that bar coasters among her father's belongings are from the Cloak and Dagger, an intelligence sting operation in 1980s New York connected to organized crime. Blum's research uncovers that a man named Barry Vincent, who fought Tim after Mercy's disappearance, is actually Ito Vincenzo, the younger brother of a convicted Mafia foot soldier who died in prison.
Lineberry takes Pine to dinner in Atlanta and reveals the full truth: Julia Pine, whose real first name was Amanda, served as an undercover informant against the Mafia, providing intelligence that contributed to the landmark 1985 RICO convictions, federal racketeering prosecutions targeting New York's Mafia families. After the family was nearly killed twice while in the U.S. Marshals' Witness Protection Program, Lineberry helped them vanish to Andersonville and followed as their protector because he had loved Amanda since before she met Tim. On the drive home, a shooter ambushes them. Lineberry is critically wounded, and Pine returns fire, damaging the attacker's vehicle. She later deduces that she, not Lineberry, was the intended target.
The investigation closes in on the Pringles. Pine discovers that Myron secretly finances pornographic films through a company called Stardust Productions, linking him to all the victims. A Pagani sports car worth approximately three million dollars, previously seen near Pine's old house, is found in the Pringles' garage. In Britta's guesthouse, however, Pine finds a shrine to the dead Pringle children, including a photo of Joe wearing the same St. Christopher's medal found on Frankie and a pornographic film starring Mary. Britta has already drowned Myron in their pool, staging his death as an accident. She holds Pine at gunpoint and explains her motive: She blames the porn industry and Myron's role in it for destroying both her children. She killed the actors she held responsible for corrupting Mary, whose overdose drove Joe to die by suicide. Britta flees in the Pagani but crashes at high speed and dies.
Pine identifies Tyler Straub, one of Lineberry's security guards, as Britta's accomplice. Straub, who began an affair with Britta at a Las Vegas tech show, carried out the physical killings of Rebane and Gillespie, planted evidence to frame Tanner, and shot at Pine on the road from Atlanta. His motive is a ten-million-dollar insurance policy on Myron's life that Britta promised to share. Straub kidnaps Tanner's seven-year-old granddaughter, Jenny, as the final victim in the symbolic family, timing the abduction to coincide with the Civil War reenactment when the town is distracted. Pine tracks Straub through an escape tunnel at the historic site. Straub shoots and kills Detective Wallis and uses Jenny as a hostage, but Laredo, using a borrowed rifle, shoots Straub in the leg. Jenny is rescued and Straub is arrested.
Pine also pieces together the truth about the night of Mercy's abduction. She deduces that her parents were at the Pringles' house that evening, not home, and Britta tearfully confirms this. Pine concludes that Ito Vincenzo, seeking revenge for his brother's imprisonment and death, watched the house, saw the parents leave, and entered through the interior door.
In the aftermath, Pine submits her DNA to genealogy databases with FBI assistance. The results deliver a shock unrelated to Mercy: Jack Lineberry is Pine's biological father. Pine confronts Lineberry at the hospital, and he confirms the truth. Pine tells him that together they must find both Mercy and her mother. Lineberry takes her hand and asks if she believes they can. Pine firmly replies that she does not think they have a choice.