Prologue. A crowded courtyard. Yahiro, a caregiver (“carer”), accompanies a man lying on a bed. She begins recounting her memories of a facility called Hailsham in which she grew up.
The scene moves back 15 years in time, to Hailsham, where children are living together. Motomu, always singled out and ignored by his classmates, throws a fit of violence when he is excluded from the soccer team, and he hits Yahiro when she tries to intervene. The teacher, Fuyuko, hearing the outburst, tries to tell the students that they are each important, and to act accordingly.
Motomu, immature and unable to communicate well with others, but he is liked nevertheless by Yahiro and her friend Suzu.
One year later, the English song “Never Let Me Go,” is playing from a stereo in Yahiro’s room, and Madame is in the room. Madame is a mysterious figure who chooses and takes away paintings and sculptures created by the children. When their works are chosen the children receive tokens as compensation, which they can trade for goods at markets. The “Never Let Me Go” tape is one that Yahiro bought using this token.
When Madame leaves, Yahiro and Motomu come out of hiding and appear in the room. While all of the children compete at making these works of art, Motomu does not have the talent. Suzu returns to the room and finds the two of them together, and as Motomu and Suzu are now lovers, she begins to question Yahiro’s motives in being alone with him.
Yahiro, left alone in the room, begins to dance to the ballad as if cradling a child. Madame, watching from a concealed place, cannot hide her excitement at the scene she is witnessing.
That summer, Yahiro and Suzu are called in by their teacher Harumi. Overhearing a conversation between the two of them where they speak about what they would like to be in the future, she confronts them with their “duties” as organ donors and whether they have accepted their places as such. “Of course,” reply the two of them.
After Harumi leaves, Suzu, who is having problems in her relationship with Motomu, asks Yahiro to mediate between them. Suzu stresses that Yahiro is Motomu’s “most trusted friend.”
After Suzu leaves, Yahiro is looking at a map of Japan, in particular a cape, “Treasure Cape,” where it is told that many things wash up on the shore. Motomu appears shortly after and Yahiro attempts to convince him to make up with Suzu. However, he explains that precisely because they only have a year remaining at Hailsham, he does not want to rush things. He instead asks Yahiro about her boyfriend, catching her off guard.
Two years later. It is winter, and the children are sent to a farm as a precursor to becoming caregivers as they await their time to become donors. The farm is located near Treasure Cape. Suzu and Motomu are lovers, however it appears that Yahiro has multiple partners.
One day, Ryota and Arisa, also living on the farm, claim to have seen Suzu’s “original” near Treasure Cape. In exchange for going to look for her, the two demand to know a secret that is known only to Hailsham graduates: “couples who truly fall in love with each other are given a “deferral” of three years’ time before becoming donors.”
The original is never found. Yahiro apologizes, explaining that they do not know about any “secret.” Motomu remains with Yahiro on the cape and tells her that he would like to look for the cassette that she once had, now lost. The two appear to enjoy each other’s company as they walk.
Two months later. Motomu has continued to draw ceaselessly since returning from the cape. He believes that his “works” will earn him a deferral. On the other hand, instead of himself who has not made any good works, he pushes Suzu away, telling her to be with another boy also from Hailsham.
Learning that Yahiro and Motomu had found the cassette on the day they went to look for Suzu’s original, Suzu insists that the Motomu has done this out of friendship for Yahiro. Yahiro applies for training as a caregiver and tells the others that she will leave the farm the next day.
Autumn, eight years later. A marshy wasteland. Yahiro accompanies Suzu who has just completed her first donation. The two have plans to meet Motomu who lives in a facility nearby.
Motomu is still doing well after his second donation. The three talk about old times. Suzu makes up her mind, and tells Yahiro and Motomu that she is sorry for deliberately sabotaging their relationship, and asks for forgiveness. Suzu recovers Madame’s address, and pleads the two of them to be interviewed for “deferral.” Together with her pleas, Motomu is given a piece of paper with an address.
One year later, at Madame’s house. Seated are Motomu and Yahiro, who has become Motomu’s caregiver. Motomu hands Madame his work and pleads his case for deferral. Madame turns to the back of the room, saying, “You have a duty to explain to them.”
Out of the back of the room appears Fuyuko the teacher, in a wheelchair. She begins to tell that Hailsham is a facility aimed at proving clone children can grow to be emotionally rich just like normal people, and to work toward ameliorating conditions for clone children. The “works” were used as part of this argument, and Fuyuko explains how they were intended to change the minds of those who would argue that clones have no heart.
Motomu demands whether this is actually an interview. Fuyuko tells him, “There is no deferral. Your life will end just as it has been delineated for you.”
Yahiro and Motomu have flashbacks of their memories at Hailsham. Motomu screams, and Yahiro holds him close.
Epilogue. The seawall at Treasure Cape. As Yahiro removes a cassette from her pocket, Motomu rushes near, replaying the day when they discover the cassette. The memory fades abruptly, Motomu disappears, and Yahiro walks away. There is a sound of a car speeding away.