As the tale begins, Coraline and her parents move into a new apartment. Coraline's parents are always busy with their work and pay her little attention. Isolated, Coraline goes off to explore. She meets the other inhabitants of the house, Miss Miriam Forcible and Miss April Spink, two elderly women retired from the stage and an even older man named Mr Bobo, who trains mice to play music. She finds a locked door in the drawing room, though the entrance beyond is bricked up. The next day she takes the key to the door, opens it, and finds a dark corridor leading to an apartment identical to her own. This alternate world is inhabited by her Other Mother and Other Father, who are near-replicas of her real parents, except they have buttons for eyes. These Other parents at first seem more interesting, fun and caring than her real parents. At the day's end, Coraline's Other Mother offers her a chance to stay in this world forever if Coraline will sew buttons over her eyes. Coraline decides she would rather go home, much to the disappointment of her Other Mother.
Upon her return to her apartment, Coraline finds her real parents are missing. They do not return by the next day, and Coraline, discovering they were kidnapped by her Other Mother, resolves to rescue them. Coraline travels again to the Other Mother's world. After angering her Other Mother by refusing to accept gifts or love, she is trapped behind a mirror as punishment. There Coraline meets the souls of three children from different eras whom the Other Mother entrapped then tossed aside when she wearied of them. After the Other Mother decides to take Coraline out of the room, Coraline challenges the Other Mother in a game to find the children's souls and her parents within the Other Parents' world, using her wits and a seeing stone received from her neighbors. Coraline finds the others' souls and escapes to the real world, forcing the door closed on the Other Mother and severing her hand. Back in her apartment, Coraline finds her parents safe and sound.
The next night, Coraline discovers her task is not done. The Other Mother's severed hand, which is still in Coraline's world as she accidentally snapped the Other Mother's hand off while closing the door, attempts to steal the key so the Other Mother can exact her revenge. Coraline lures the hand to a well and tricks it into falling in with the key, ridding the world of the danger of the Other Mother forever.