Set in an alternate 1979 England where World War II ended through negotiated peace after Hitler's assassination in 1943, the novel follows Vincent, a 13-year-old boy who lives with his identical triplet brothers, Lawrence and William, at Captain Scott Home for Boys in the New Forest. The Home is one of several "Sycamore Homes" established after the war. The boys are told they are special orphans whose parents died of heart attacks. Three rotating caretakers, Mother Morning, Mother Afternoon, and Mother Night, work in shifts. The manor is enclosed by a high flint wall topped with broken glass; the boys' only education comes from
The Book of Knowledge, an eight-volume children's encyclopedia. Mother Morning records their dreams in The Book of Dreams, while their misdeeds are logged in The Book of Guilt. The boys receive constant medication for a mysterious illness called "the Bug." Over the years, dozens of other boys have either died or departed for Margate, a seaside resort they believe houses recovered children. The triplets are the last residents. In March 1979, all three begin dreaming of a skinny, barefoot girl with long black hair. In William's version, the dream involves a knife and blood.
A parallel narrative introduces Nancy, who turns 13 in Exeter. Her parents, Kenneth and Marjorie Fletcher, have never allowed her to leave their bungalow. Television is her only window to the outside world. Her parents insist the world is too dangerous but offer no explanation.
Sylvia Dalton, the Minister of Loneliness in the new Conservative government, announces plans to close the Sycamore Homes and place the children with adoptive families. Dr. Roach, an elderly scientist who has examined the boys their entire lives, protests furiously. The Minister visits Captain Scott and organizes "Socialization Days" with girls from another Home. At the first, Vincent meets Jane, a sharp, pale girl from Edith Saunders Home for Girls, who whispers a revelation: The medicine does not make them better. It makes them sick. Vincent secretly stops taking his pills, and within days his symptoms vanish. William follows suit and improves, while Lawrence, still medicated, grows worse.
When Mother Morning discovers Vincent's hidden pills, she forces him to swallow five at once, triggering a severe delirium. During his illness, Mother Night whispers urgently that he must get a family to take him and must never go to Margate. Shortly after, Mother Night vanishes and is replaced by a near-identical substitute.
On a village errand, Mr. Webb, a friendly baker, thanks Vincent for saving his grandson's life: A chemotherapy drug tested on Sycamore children cured the boy's cancer. Vincent realizes the Bug does not exist: The children were never sick, and boys who died were killed by the experimental medications. At the second Socialization Day, Vincent confides in Jane, and during the outing William sexually assaults Karen, one of the girls from Edith Saunders Home. Vincent finds her afterward and persuades her to stay silent. He later learns that Jane has been sent to Margate.
The Minister visits serial killer Arthur Powell in Strangeways Prison. Powell, convicted of torturing and killing 11 schoolgirls in the 1950s, has learned that three identical copies of himself exist. He demands to meet them in exchange for revealing the burial location of Nancy Liddell, his only victim whose body was never found. The Minister brings the boys to the prison, telling them their father survived the heart attack they were told killed him. Powell is executed on August 31, 1979, without honoring his promise.
That same morning, Nancy's parents throw a party at eight o'clock, the moment of Powell's execution, with a three-tiered cake and Babycham, a sparkling pear drink. When Nancy watches a television clip of the triplets, her parents recognize Powell's features in the boys' faces. A government catalog of Sycamore children arrives, and her parents fixate on the triplets.
The Fletchers request a home visit. At their bungalow, the boys are enchanted by Kenneth's model village, but William attacks Lawrence in a violent fight. As Vincent returns alone, he glimpses a girl with long black hair in a window. She mouths a single word: "Run."
Nancy searches her parents' loft and finds newspaper clippings about Powell and photographs of a girl identical to her. She confronts her parents, who reveal that Nancy Liddell was their firstborn daughter, murdered by Powell in 1951. They moved away, changed their names, and had Nancy made as an illegal copy of their dead child. They have ordered one of Powell's copies not to adopt but to torture and kill, recreating what Powell did to their daughter.
Vincent discovers the missing encyclopedia page, hidden by the original Mother Night with a note: "I thought you should know." The entry, headed "Copy," explains that the Sycamore children are human clones created by Dr. Roach from prisoners' genetic material. Mother Morning confirms the truth: The boys are copies of a criminal, and their caretaker mothers are copies too.
The Fletchers choose William. In an Ethical Hour, the boys' guided moral discussion session, Vincent poses the question of whether William should go if there might be danger. Lawrence volunteers to take William's place, wearing William's red clothes. Vincent allows this swap because he cannot bear to lose William, whom he has always loved best.
At the Fletchers' house, Lawrence has been drugged. Nancy watches her parents prepare a room with plastic sheeting, ropes, and knives. She escapes the bungalow for the first time in her life, hitchhiking to Ashbridge, where she climbs the flint wall by standing on a wild pony's back and finds Vincent. He calls the Minister, who contacts the police. They raid the home and find Lawrence alive but severely injured: His tongue has been severed.
The Minister is forced to resign; the Prime Minister reveals to her that "Margate" was the code name for gassing children deemed dangerous in locked vans. The identity swap comes to light: The injured boy is Lawrence, not William. Vincent confesses he knew about the danger but let Lawrence go because he loved William more. Lawrence writes on a notepad: "Vincent did this to me. It's all his fault." At 14, Lawrence runs away and is later found living on the streets of London with a heroin addiction. Vincent searches for years but never finds him.
The narrative jumps to 2019. Vincent, now a librarian, visits Margate with Nancy, his partner. At an exhibition about the Sycamore Scheme, placards detail the full history: copies bred from criminals for drug trials, dreams monitored to predict violence, children exterminated in gas vans. Sylvia Dalton is credited with decades of campaigning that secured equal rights for copies at the cost of her political career. Vincent finds Jane White's last entry in a Book of Guilt: She was written up for encouraging a Captain Scott boy to stop his medicine. He realizes his own actions sealed Jane's fate: He told William what Jane said, William told Mother Morning, and Mother Morning reported Jane. The volunteer beside the cabinet is Mother Night, Frances, now in her seventies, released after a decade in prison. She recognizes Vincent, and they embrace. The novel ends on the Margate shoreline at sunset, the sea erasing their footsteps as Vincent, Nancy, and Frances walk west beneath the word DANCING.