Coraline is a young girl who has just moved into a new apartment with her parents. As Coraline acclimates to her surroundings before the school year begins, she acquaints herself with her eccentric new neighbors. In the flat below Coraline’s apartment, two older women named Miss Spink and Miss Forcible live with their dogs. In the apartment above Coraline’s lives a “crazy old man” who claims to be training a mouse circus. Although Coraline’s parents work from home, the protagonist often feels lonely and isolated. As a result, Coraline must find ways to entertain herself and make fun out of mundanity.
One day, Coraline decides to explore her own apartment. She is especially intrigued by the door in the corner of the drawing-room, which only opens onto a brick wall. One night while she is lying awake in her bed, Coraline hears a mysterious sound coming from down the hall. She investigates and realizes that the old door to the drawing-room is slightly ajar. After her exploration, she experiences weird dreams. The next day, she experiences a series of strange events. Coraline runs into the man that lives above her apartment, and he tells her that the mice have advised Coraline not to go through the door. Then, Coraline heads to Miss Forcible and Miss Spink's apartment, where the women warn her that she is in grave danger. Coraline is pleased by her neighbor's prophecy, as she is looking for excitement in her boring life.
The following day, Coraline is left alone in the house while her mother is grocery shopping. Bored and lonely, Coraline decides to take the set of keys and head into the empty drawing room. She unlocks the blocked door, only to find that the bricks have disappeared. Coraline walks through the door and heads down the dark hallway. Upon entering the hallway, Coraline is struck by how closely the empty flat resembles her own. The wallpaper, carpet, and pictures all appear identical to the items in her apartment. Coraline hears a voice that sounds as if it belongs to her mother. She follows the voice and heads down the corridor.
Coraline discovers a woman in the kitchen that looks like her mother—with a few differences. The woman is taller, thinner, pale, and has black buttons in the place of her eyes. It appears that Coraline has encountered a world that is an alternate version of her reality, complete with an "other mother" and "other father." While exploring the outside of her house in the other world, Coraline encounters a black cat. Coraline begins conversing with the cat, but she finds the creature to be rude and cold. She then enters Miss Spink and Miss Forcible's apartment in the other world.
Coraline finds that their apartment has been transformed into a theater, and one of the neighbor’s black Scottie dogs asks Coraline for a “ticket” to the show. Miss Spink and Miss Forcible then shed their “recognizable skin” and emerge as thin, pale women with black button eyes. The performance is strange, and Coraline is scared by the characters in the alternate world. Her other mother and other father tell Coraline that she can stay in this world forever if she replaces her eyes with black buttons. Terrified, Coraline returns back to the real world, but she finds that her parents have gone missing. After Coraline receives a message that her real parents are endangered, she is forced to rescue them from the other world.
After further investigation, Coraline realizes that her other mother is the creator of the other world and has trapped various children inside of it over the years. In order to free all of the captured souls that are stuck in the other world, Coraline negotiates with her other mother. They decide that if Coraline successfully locates the three souls and her parents within the other world, everyone can be set free. Coraline sets out to locate each of the three missing souls. She is met with challenges along the way, but she successfully overcomes all of her fears and finds the missing souls. In addition, Coraline finds that her parents are trapped within a small snow globe that rests on the mantelpiece in the other world.
Although the other mother had previously agreed to let Coraline go if she successfully completed her challenges, the other mother does not hold up her end of the deal. Instead, Coraline is forced to narrowly escape from the other world. Safe and sound in the real world, Coraline realizes that her parents never noticed that she had gone missing. At night, she dreams that her victory against the other mother is not yet complete, as the other mother's hand has escaped into the real world. Coraline successfully traps her other mother's hand, and it falls into a well. The other mother has officially been defeated. In the last scene of the novel, Coraline visits her neighbors, who acknowledge that balance has finally been restored in their lives due to the villain’s demise. Coraline falls asleep in her bed before beginning her first day of the new school year.