Twelve-year-old Bethany Cole narrates a story that begins with her parents abruptly uprooting her from their home in Greenleaf, Pennsylvania, driving for hours across unfamiliar states without explanation. Her mother, Hillary, sobs silently in the front seat, a behavior constant since the previous summer. Her father, Walter, drives in grim silence. Bethany describes her parents as old, fragile, and intensely overprotective: They have never hired a babysitter, never allowed a sleepover, and have kept her close every moment of her life.
They arrive late at night at a dark house. A white-haired woman answers and embraces Walter warmly. From the car, Bethany overhears her father say, "She doesn't know anything about Elizabeth," a name that strikes her as deeply significant, though she has no idea who Elizabeth is. Walter tells Bethany she will stay with "your aunt Myrlie," stunning her, since she believed all her parents' siblings were dead. Hillary clings to Bethany in a desperate embrace before Walter peels her away. When Bethany asks if they will return for her birthday, Walter stares in horror and leaves without answering. Myrlie gasps at the sight of Bethany: "You just look so much like . . ." She trails off.
Bethany tries calling her parents, but every number has been disconnected, and no directory listing for any Cole in Greenleaf exists. The next morning, she deduces from a facial resemblance that Myrlie is Hillary's sister. When Walter calls, he refuses to reveal his location. Bethany eavesdrops on Myrlie's subsequent conversation with him and hears her argue that Bethany "needs to know about Elizabeth," but Walter refuses.
As Bethany adjusts to life in Sanderfield, Illinois, people react to her appearance with unsettling shock. At the local YMCA, a woman stares and murmurs, "You just look so much like someone I used to know." Bethany connects these reactions to the mysterious Elizabeth. Myrlie, too, anticipates Bethany's food preferences with uncanny precision, further unsettling her.
The breakthrough comes when Hillary calls in the middle of the night, addressing Bethany as "Elizabeth" and refusing correction. She warns against going to Sinclair Mountain for Elizabeth's birthday because of a terrible dream. Walter takes the phone, admits Hillary is reacting badly to medication, and under Bethany's pressure, whispers that Elizabeth was real. He directs Bethany to ask Myrlie and gives Myrlie permission to tell the story.
Myrlie reveals that Elizabeth was Bethany's older sister, born in June 1978. Myrlie's own daughter, Jocelyn ("Joss"), was born two months later. The cousins were inseparable and gifted gymnasts tipped for the 1992 Olympics. On Elizabeth's thirteenth birthday, both families visited Sinclair Mountain, a large amusement park. On the drive home, an accident killed Elizabeth and Myrlie's husband, Thomas Wilker. Joss was badly injured. Hillary, who was driving, believed the crash was her fault, though this was never confirmed. Walter and Hillary left Sanderfield and severed contact, unable to bear seeing Myrlie still had a daughter when theirs was dead. Bethany begins reinterpreting her entire life: her parents' overprotectiveness, their refusal to let her take gymnastics, and their ability to predict her developmental milestones.
Joss, now a minister in St. Louis, visits and shares memories of Elizabeth. She inadvertently refers to "Elizabeth Krull," revealing the family's original surname was Krull, not Cole. Walter then sends a package containing guardianship documents signed under multiple aliases, birth certificates for Bethany under each surname listing the same date but different birthplaces, and $10,000 in cash. On the money wrapper, Bethany finds a fragmented letter: "He is chasing me. He is hunting me down. . . . Lies were the only way to get Bethany. . . . We made a deal with the devil and now the devil is demanding his due."
During another nighttime call, Hillary again believes she is speaking to Elizabeth and tells her, joyfully, that Walter has found a way to bring her back: "We'll make a copy of you. . . . A clone." Bethany drops the phone and faints. When she recovers, Joss, a biology major, confirms that human cloning was theoretically possible. Bethany screams that she is not a clone and flees into the dark streets.
Joss finds Bethany collapsed near the courthouse. Bethany asks whether Elizabeth liked swimming. Joss reveals Elizabeth nearly drowned as a child and was terrified of water, while Bethany loves it. Bethany clings to this difference as evidence she is not merely a copy. A black rental car pulls up, and a man in shadow calls both of them by name, but a police car arrives first, driven by Officer Ryan Bridgeman, a childhood friend of Joss's.
Researching online, Bethany connects her father to Dalton Van Dyne, a recently released embezzler who ran a company called Digispur. "Walter Krull" appears as a fictitious employee in company records. She also finds an old interview in which Van Dyne endorsed human cloning, saying the first person to produce one would "be hailed as a modern god." Bethany theorizes Van Dyne funded Walter's research and now wants to expose her as proof.
On Halloween, Van Dyne appears at Myrlie's door, addressing Bethany by name. Officer Bridgeman confirms Van Dyne has relocated to Sanderfield, and the FBI begins monitoring him. During a violent storm, Hillary calls to say goodbye, believing Bethany will die at thirteen as Elizabeth did: "We'll lose you at thirteen too. . . . It's just meant to be." Lightning cuts the call. Bethany breaks down, chanting, "I am not Elizabeth!"
Joss coaxes Bethany to the town's annual Harvest Festival. Bethany goes wearing prescription swim goggles and a swim cap, claiming her identity as a swimmer. At the festival, she spots her parents in the crowd. Before they can reach each other, Van Dyne appears and confronts Walter: "Where is he?" He reveals his true motive: He has spent 13 years in prison longing for his own clone, a "younger self" he believed Walter created. Bethany realizes Van Dyne paid Walter to clone Van Dyne himself, but Walter used Elizabeth's frozen cells instead. She removes her disguise and declares: "Your clone doesn't exist. They made me instead. I am the clone." Van Dyne begins to cry.
The epilogue, set months later, reveals the full truth. Walter approached Van Dyne in the late 1990s promising to produce a clone, and Van Dyne funded a secret lab. When Van Dyne was arrested, Walter chose to use Elizabeth's cells. Four cloned embryos were implanted in surrogate mothers; three babies died within a day, and the fourth survived: Bethany, carried by Hillary herself. Walter told everyone the clones had died, changed his name, and disappeared. The family undergoes therapy, and Bethany enrolls in Sanderfield Middle School. In the final scene, all five family members plant a ginkgo tree in Myrlie's backyard, following a family tradition of planting a tree for each new baby. Bethany chose the ginkgo because it is a unique species that has survived against the odds. The sign at its base reads, "Bethany Elaine Cole, Born November 2," with no year, because Bethany considers herself to have two birthdays: the day she was born and the day she faced the truth about who she is.