The film begins with onscreen captions explaining that a medical breakthrough in 1952 has permitted the human lifespan to be extended beyond 100 years. Subsequently, the film is narrated by 28-year-old Kathy H. as she reminisces about her childhood at Hailsham, as well as her adult life after leaving the school.
The first section of the film depicts young Kathy, along with her friends Tommy and Ruth, spending their childhood at Hailsham, a seemingly idyllic English boarding school. It is subtly revealed that the film is set in an alternate twentieth century. A teacher is fired after telling the pupils of their fate: they exist to provide donor organs for transplants. They will be nurtured to adult age, then they will be available for "selection." After their third "selection" they will "complete" before they can be selected for any more procedures. Some "complete" after their first "selection", while others survive four or more "selections." Tommy is emotionally angry and is teased by the other boys. Kathy falls in love with him.
In the second section of the film, the three friends, now teenagers, are rehoused in cottages on a rural farm. They are permitted to leave the grounds if they wish. They do not question the ethics of their situation. At the farm, they meet other graduates of similar places. Kathy, Tom and Ruth are clones who are fascinated by the idea of finding the original people that they were "modeled on". Kathy and her friends are questioned about rumours of the possibility of "deferral," which allows couples several extra years before being "selected" if they are in love and can prove it. Tommy reasons that the art gallery at Hailsham was intended to identify clones who have a soul. Tommy and Ruth become lovers. The lonely Kathy applies to become a "carer", a clone who is taught to drive and trained to give post-operative care to other clones. In exchange for supporting and comforting donors after their organs are harvested, she gets a temporary reprieve from selection. She has become a carer by the time she hears that Tommy and Ruth have split up.
In the third section of the film, Kathy has been working as a carer for several years. She has watched many clones "complete." She reunites with Ruth, who is frail after two "selections". Ruth has been keeping track of Kathy and Tommy, and helps Kathy arrange their reunion. Ruth admits that she did not love Tommy and seduced him because she was jealous and afraid to be alone. She is consumed with guilt, and has been searching for a way to help Tommy and Kathy. She believes that Tommy and Kathy would qualify for "deferral." She gives them the address of "Madame," who regularly visited Hailsham and selected student artwork to go into the gallery. Ruth "completes" on the operating table shortly afterward. Tommy tells Kathy that he has been creating art for several years in hopes of a deferral. He and Kathy drive to visit Madame, and learn that deferral does not exist. Tommy's artwork will not help them.
The film ends after Tommy has "completed," leaving Kathy alone. Two weeks after losing Tommy, Kathy is notified that her first "selection" will occur in one month. Contemplating their childhood, she speculates whether their fate is really so different from the people who receive their organs. "We all complete. Maybe none of us really understand what we've lived through, or feel we've had enough time."