The first part, "The Thieving Magpie", begins with the narrator, Toru Okada, a low-key and unemployed lawyer's assistant, being tasked by his wife, Kumiko, to find their missing cat. Kumiko suggests looking in the alley, a closed-off strip of land behind their house. After Toru stays there for a while with no luck, May Kasahara, a teenager who had been watching him camping out in the alley for some time, questions him. She 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 to crawl into and think. Toru receives sexual phone calls from a woman who says she knows him. He also receives a phone call from Malta Kano who asks to meet with him.
Kumiko calls Toru to explain that he should meet with the clairvoyant Malta Kano, who will help with finding the cat. Malta Kano had come recommended by Kumiko's brother, Noboru Wataya, which is also the name given to the cat. Kumiko's family believes in fortune-telling and had previously stipulated that the couple meet with an elderly man, Mr. Honda, for consultations on a regular basis, which they did for some time. (Instead of giving advice, he spends most of their sessions retelling the same story of his experience in the Kwantung Army in the lost tank battle with the Russians at Nomonhan on the Manchukuo-Russian border during World War II.) Toru meets the mysterious Malta Kano at a busy hotel restaurant, and she tasks her sister Creta Kano to further the work. Both sisters wear unusual clothing: Malta a large red hat and Creta unstylish 1960's clothing. Creta meets Toru at his home and begins to tell him the story of her past, involving being raped by Noboru, but abruptly leaves. Toru notices Kumiko is wearing perfume that has been gifted to her by some unknown person. The cat remains missing. Toru is contacted by Lieutenant Mamiya, who informs Toru that Mamiya's old war friend corporal Honda has died and that Mamiya wishes to visit Toru to drop off an item that Honda had bequeathed to him. The first section ends with Lieutenant Mamiya arriving and telling Toru a long tale about his eerie and mystical wartime experiences in Manchukuo in the Kwantung Army, where he sees a man skinned alive. Mamiya was also left to die in a deep well before being saved by corporal Honda. The gift from Honda is an empty box.
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 its power is never fully 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 and 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 agent 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. She reveals that she did not cheat on Toru with just one man, but in fact there were several. Noboru's obsession with their middle sister, continued with Kumiko, triggered sex addiction in her until Noboru stepped in. Subsequently, in a discussion between Toru and May, Toru says Kumiko was successful in killing Noboru and is now serving time in jail after admitting the deed — time of her own volition, because she is waiting for the media circus to end so neither she nor Toru are targeted. Toru says that he will wait for her, and bids May goodbye.
