The first part, "The Thieving Magpie," begins with Toru Okada, a low-key unemployed man, who is tasked by his wife, Kumiko, to find their missing cat. Kumiko suggests starting by looking in the alley, a closed-off strip of land existing behind their house. After hanging out there for a while with no luck, May Kasahara, who had been watching him camping out the alley for some time, questions him. She then invites him over to her house in order to sit on the patio and look over an abandoned house that she says is a popular hangout for stray cats. The abandoned house is revealed to possibly contain some strange omen, as it had brought bad luck to all of its prior tenants. It also contains an empty well, which Toru uses later on to crawl into and think.
With Toru having been unsuccessful in finding the cat, Kumiko asks her brother, Noboru Wataya, for help. Her side of the family (though her not so much) all believe in fortune-telling and other clairvoyant-like skills. Noboru recommends Malta Kano, and she and her assistant sister, Creta, help Toru in finding the cat using their vague insight of the future. Creta meets Toru and begins to tell him the story of her past, involving being raped by Noboru. Among other events that occur, Toru notices one day that Kumiko is wearing perfume that has been gifted to her by some unknown person. The cat remains missing, and the first section ends with Lieutenant Mamiya telling Toru about his wartime experiences.
Kumiko is revealed to be missing at the start of the second part, "Bird as Prophet." Shortly after, Toru finds out through a meeting with Noboru and Malta that Kumiko has apparently been spending time with another man and wants to end her relationship with Toru. Confused, Toru tries several things to calm himself and think through the situation: talking and taking up work with May Kasahara, hiding at the bottom of the well, and loitering around the city looking at people. Work with May involves tallying up people with some degree of baldness at a subway line for a wig company. While at the bottom of the well (of the abandoned house), Toru reminisces about earlier times with Kumiko, including their first date to an aquarium where they looked at jellyfish. He also experiences a dreamlike sequence where he enters a hotel room and speaks with a woman, and notices a strange blue mark on his cheek after he leaves the well. While loitering in the city, he spends most of the day sitting outside a donut shop and people-watching. Through this activity Toru encounters a well-dressed woman and also a singer he recognizes from his past, whom he follows and beats with a bat after getting ambushed by him.
"The Birdcatcher," the third, final, and lengthiest part, ties up most loose ends while introducing a few new characters. The well-dressed woman Toru met while people-watching is revealed to be Nutmeg, whom he sees again when he reverts to people-watching. She hires him to relieve clients, middle-aged or older women, of some kind of inner turmoil that develops inside of them. The blue mark is involved in this somehow, though it is never really explained. In return, Toru receives pay and partial possession of the abandoned house that had been purchased to resell by some property agency. Cinnamon, Nutmeg's son, maintains the house and refits the well with a ladder and pulley to open/close the well cap from the bottom. Toru periodically goes to the bottom of the well to think and attempt to revisit the hotel room. The cat, who has been hardly mentioned following Kumiko's disappearance, shows up at Toru's home after nearly a year of being missing. Toru discusses Kumiko's disappearance with Noboru directly and indirectly (through his mole Ushikawa) and eventually arranges for a talk with her through the Internet, using her recollection of the jellyfish date as a means to verify her identity.
Finally, Toru is able to travel to the hotel room from the well and confronts the woman, realizing that she is Kumiko and breaking the spell. It is revealed in this reality that Noboru has been beaten into a coma by a bat, with the assailant described to look just like Toru. An unknown man enters the hotel room and attacks Toru, the intruder, with a knife. Toru fights back with the bat and kills the man, before escaping back to the well. In the well, bruised and unable to move, Toru passes out after the well fills with water. Cinnamon saves him, and some days later Nutmeg notifies him that in this reality Noboru had a stroke and is now in a coma. Kumiko sends him a message on the computer to let him know she is alright but intends to kill Noboru by pulling the plug on the life support. It is revealed in a meeting between Toru and May that Kumiko has been successful and is now serving time after admitting to the deed. Toru says that he will wait for her, and bids May goodbye.