A medical breakthrough has extended the human lifespan beyond 100 years. In 1978, the young Kathy H, along with her friends Tommy D and Ruth C, spend their childhood at Hailsham, a traditional boarding school. The teachers, called guardians, encourage students to be health-conscious and create artwork, the best of which is accepted into The Gallery run by the mysterious Madame; they have little other contact with the world beyond the school's fences. Miss Lucy, a perceptive new guardian, tells her class that they exist to be organ donors and are destined to die, or complete, early in their adulthoods; she is quickly fired by the headmistress, Miss Emily. As time passes, Kathy grows attracted to Tommy, but Ruth wins him for herself despite having engaged in his teasing.
Seven years later, Kathy, Ruth and Tommy, now young adults, are rehoused in the Cottages on a farm; they are allowed to drive away on day trips, but they remain reclusive, lacking social skills and resigned to their fate. The trio meet others from similar schools who claim that Hailsham students are privileged, and it is revealed that they are all clones. They discuss rumours of deferrals to organ donations that might be granted to clones who are in love, and the nature of the people they were cloned from, whom they unsuccessfully search for in books and out at the seaside. Tommy, still partnered with Ruth, is convinced that The Gallery serves as verification for deferrals, since artwork reveals the soul, and laments his lack of creativity. Ruth spites a lonely Kathy, claiming that Tommy never thought of her as more than a friend; Kathy leaves, enlisting as a postoperative carer for fellow clones.
Another nine years later, Kathy has watched many donors gradually die as their organs are harvested. Having not seen Ruth or Tommy since she left the Cottages, she comes across Ruth, frail after two donations. They seek out Tommy to make a nostalgic seaside trip. Ruth reveals that she only seduced Tommy because she was afraid to be alone; she is consumed with guilt and wishes to help Tommy and Kathy seek a deferral. She leaves them with the address of Madame, whom she believes has the power to help them, and soon dies on the operating table. Kathy and Tommy finally enter a relationship, and Tommy explains to Kathy, now his carer, that he has been creating artwork in the hope that it will earn them their deferral. The couple successfully bring it to Madame, but she remains distant, suddenly inviting Miss Emily to speak. They reveal that deferrals are indeed a myth, and that the gallery was created to affirm the basic humanity of clones as an appeal for their ethical treatment; Hailsham, now shut down, was the last institution to value young clones as "all but human". Kathy and Tommy leave in disappointed silence, but Tommy explodes with grief and anger mid-journey, as he used to as a child. Tommy dies on his fourth donation, leaving Kathy alone as hers begin. Contemplating the ruins of her childhood, she questions in voice-over how different her life has been from normal people's.
