Coraline Jones and her parents move into an old house that has been divided into flats. The other tenants include Miss Spink and Miss Forcible, two elderly women retired from the stage and Mr. Bobo, initially referred to as "the crazy old man upstairs," who claims to be training a mouse circus. The flat beside Coraline's is unoccupied, and a small door that links them is revealed to be bricked up when opened.
Coraline goes to visit her new neighbours. Mr. Bobo relays to her a message from his mice: "Don't go through the door." Coraline also has tea with Miss Spink and Miss Forcible, and Miss Spink spies danger in Coraline’s future after reading her tea leaves.
Despite these warnings, Coraline decides to unlock the door when she is home by herself. This time, she finds the brick wall behind the door is gone. In its place is a long hallway that leads to a flat identical to her own, except inhabited by the "Other Mother" and "Other Father," who have black buttons for eyes. The Other Mother is notably taller and thinner than her real mother. Her black hair seems to move by itself, her skin is paper-white, and her nails are long and red. Coraline finds the "Other World" more interesting than her own; the Other Mother cooks food that she actually enjoys, both of her Other Parents pay more attention to her, her toy box is filled with animate toys that can move and fly, the Other Miss Spink and Miss Forcible perform a never-ending act in their flat, and the Other Mr. Bobo performs a mouse circus.. She even finds that the feral black cat that wanders around the house in the real world can talk. The cat identifies itself as the same cat that lives in the real world, and possesses the ability to travel through the gaps between the two worlds. Although intentionally rude and unhelpful for the greater part of the conversation, it briefly praises her for bringing "protection," then vanishes.
After Coraline returns to the copy of her flat, the Other Mother offers Coraline the opportunity to stay in the Other World forever, but in order to do so, Coraline must allow buttons to be sewn into her eyes. Coraline is horrified and returns through the door to her home. Upon return to her apartment, Coraline finds that her real parents are missing. They do not return the next day, and the black cat wakes her and takes her to a mirror in her hallway, through which she can see her trapped parents. They signal to her by writing "Help Us" on the glass, from which Coraline deduces the Other Mother has kidnapped them. Though frightened of returning, Coraline goes back to the Other World to confront the Other Mother and rescue her parents. In the garden, Coraline is prompted by the cat to challenge the Other Mother, as "her kind of thing loves games and challenges." The Other Mother tries to convince Coraline to stay, but Coraline refuses, and is locked within a small space behind a mirror as punishment.
In the small dark closet space, she meets three ghost children. Each had in the past let the Other Mother, whom they archaically refer to as the "beldam," sew buttons over their eyes. They tell Coraline how the Other Mother eventually grew bored with them, leaving them to die and cast them aside, but they are trapped there because she has kept their souls. If their souls can be rescued from the Other Mother, then the ghosts can pass on. The ghost children implore Coraline to escape and avoid their fate.
After the Other Mother releases Coraline from the mirror, Coraline proposes a game: if she can find the ghost children's souls and her parents, then she, her parents, and the ghost children may go free. If she loses, then Coraline will let the Other Mother sew the buttons into her eyes and become a loving daughter to her. The Other Mother agrees and they both swear on their right hands.
Coraline searches through the Other World and overcomes the Other Mother's obstacles by using her wits and Miss Spink's lucky stone (the protection the cat referred to) to find the marble-like souls of the ghost children. She also deduces that her parents are imprisoned in a snow globe on the mantelpiece. The ghost children warn her that even if Coraline wins, the Other Mother will not let them go, so Coraline tricks the Other Mother by announcing that she knows where her parents are hidden: in the passageway between the worlds. The Other Mother cannot resist gloating by opening the door to show Coraline that her parents are not there. When the Other Mother opens the door Coraline throws the cat at the Other Mother, grabs the snow globe, and escapes to the real world with the key, and the cat quickly follows. While escaping, Coraline forces the door shut on the Other Mother's hand. Back in her home, Coraline falls asleep on a chair. She is awoken by her parents who have no memory of the events.
That night, Coraline has a dream in which she meets the three children at a picnic. The children are dressed in clothes from different periods and one seems to have wings. They warn her that her task is still not done: the Other Mother will attempt to get her back and will try to get the key to open the door between the worlds. Coraline goes to the old well in the woods to dispose of the key. She pretends to have a picnic, with the picnic blanket laid over the entrance to the well. The Other Mother's severed hand attempts to seize the key, but steps on the blanket and falls into the well. Coraline returns to the house, greeting her neighbours (who finally get her name right), and getting ready for school tomorrow.