The novel is divided in three sections that chronicle the phases of the main characters’ lives.
This section is set at the fictional Hailsham boarding school in East Sussex, England. It is clear from the peculiar way the teachers—known as “guardians”—treat the students, that Hailsham is not a normal boarding school. Eventually, it is revealed to the reader and to the students that the children are clones created to provide vital organs for non-clones (“originals”). The students are not taught any life skills, though the teachers encourage the students to produce various forms of art and poetry. The best works are chosen by a woman known only as “Madame,” who takes them away. Students believe she keeps their work in a secret Gallery although this is not discussed with guardians.
The three main characters—Ruth, Tommy and Kathy—develop a close friendship. From a young age, Kathy seems to have resigned herself to being a rather passive observer of other people and the choices they make, instead of making her own. Tommy, an isolated boy who struggles to be creative, is often the target of bullies. And while Ruth is an extrovert with strong opinions who appears to be the center of social activity in her cohort, she is not as confident as she is perceived to be. Early on in the story, Kathy develops a fondness for Tommy, looking after him when he is bullied.
Although a bond grows between Kathy and Tommy, their relationship doesn’t become physical. Instead, Ruth and Tommy enter into a sexual relationship, as many of the students do. At one point, they break up, and Kathy resolves to begin a relationship with Tommy, with many of the fellow students seeing it as the normal course of events. But Ruth asks Kathy to talk to Tommy in order to patch things up between herself and Tommy, so instead of asking for a relationship between herself and Tommy, Kathy ends up interceding to get Tommy to take Ruth back. Ruth and Tommy remain together throughout their remaining time at Hailsham.
In the second section, the characters, who are now young adults, around age 16 – 18, have moved to the “Cottages,” residential complexes where they begin contact with the external world. It is clear from the descriptions of the Cottages that they are vastly inferior to the luxuries of Hailsham. The buildings are cold and in poor condition, and there is little for the clones to do there, with no supervision apart from one maintenance man. The romantic relationship that had developed between Ruth and Tommy continues, while Kathy explores her sexuality with other students there without forming any long-term relationship. Kathy often takes the role of the peacemaker in the tumultuous relationship between Tommy and Ruth.
During their time at the Cottages, the characters travel to Norfolk, where two of their housemates tell them of a rumor that Hailsham students might be allowed to “defer” from being donors for three years if they have truly fallen in love. Tommy hypothesizes that Madame collected their art for her Gallery to use it as a kind of lie detector. The art would tell administrators whether clones are telling the truth about being in love, via their personality that they reveal through their art. Tommy feels great anxiety about this issue, because he was always bad at art; he was told that it wasn’t important if his art was any good, but then later told that it was important. Thus he began working on his art in secret in order to convince Madame that he is capable of being truly in love.
Tensions among Tommy, Ruth, and Kathy rise as they all struggle to find acceptance and understanding outside Hailsham and with each other. Among these tensions is Kathy’s hypothesis and Ruth’s outburst that children such as themselves were modelled from the human “trash” of the Earth. These complications inevitably lead to Kathy requesting early departure from the cottages to become a “carer”—a clone who cares for other clones recovering from organ-removal surgery.
The third section involves Tommy and Ruth becoming donors and Kathy becoming a “carer.” About ten years go by without Kathy seeing Ruth or Tommy. Towards the end of this time Kathy sees her old classmate Laura, who is also a carer, and they speak. The reader learns from their conversation that Hailsham has recently closed and that Ruth is on her first donation, which did not go well, and her health has deteriorated. Kathy begins to care for Ruth, and Ruth is aware that the next donation will most likely be her last. She suggests to Kathy that they take a trip and, knowing that Tommy is in a nearby facility, bring Tommy with them. Kathy and Ruth pick up Tommy at his hospital, and they drive to see an abandoned boat in the middle of a marshland.
During this trip, Ruth expresses regret and vocalizes what had been only earlier implied: she used deliberate manipulations to come between Kathy and Tommy despite sensing their bond. In an effort to make amends, Ruth hands them a piece of paper with Madame’s address, and urges them to pursue a relationship with one another and seek a deferral. Tommy seems puzzled yet excited about the possibility of getting a deferral, while Kathy seems skeptical and afraid to be too hopeful. Soon after the trip, Ruth makes her second donation and dies, which is euphemistically referred to as “completion” by the characters. The term is also referring to the fact that they have given all that they have; their purpose in life is complete.
Kathy then becomes Tommy’s carer and begins a romantic relationship with him. For a time they are happy, but then think again about the possible deferral. Tommy selects pieces of his art to show to Madame, and, encouraged by Ruth’s last wishes they go to Madame’s address. Their goal is to see if they can defer Tommy’s fourth donation (which is often the last one). Tommy has brought his art with him, as evidence of his personality, to back up his claims that he and Kathy are in love. Madame leads Kathy and Tommy inside, where they also meet Miss Emily, their old headmistress. They learn that Hailsham was a failed effort on their part to prove to society that clones had souls. They emphasized art as a means to make this point to the world. However, the experiment ultimately failed to achieve what they had wanted and they lost their funding and Hailsham had to be closed. Other clones were raised in much grimmer circumstances. Miss Emily dismisses the rumor that Hailsham students may defer their donations if they fall in love.
The pair learn that Hailsham was an experiment to improve the living conditions and alter societal attitudes toward clones. Until Hailsham, society had preferred to view clones merely as non-human sources of organs. Kathy and Tommy learn that Miss Emily actually was disgusted by the clones, and that Miss Lucy (another teacher at Hailsham) was dismissed for her dangerously open attitudes towards them. Tommy is upset and bewildered by the discovery of the purpose of Hailsham, whereas Kathy appears simply humbled, as if she has passively accepted her fate. The novel ends after Tommy’s “completion” (i.e. death), on a note of resignation, as Kathy will now become a donor and eventually “complete”.