Toru Okada quits his job as a gofer in a Tokyo law firm and stays home to take care of the house while his wife works. Toru and Kumiko have been married for six years. The Okadas have an insular, childless marriage. They live in Tokyo with their cat, Noboru Wataya. Toru's quiet life changes a few days after their cat disappears and he meets an unusual cast of characters who help him explore connections between waking and dreaming, past and present, good and evil. Once the search for the wayward feline begins, Toru befriends teenager May Kasahara. Not long after meeting May, Toru meets Malta Kano, an unusual psychic whose trademark is a red vinyl hat. Malta is named after the island, as is her younger sister Creta Kano. Next, Toru makes the acquaintance of Lieutenant Mamiya, a former soldier in the Japanese army during World War II. Mamiya and Toru are brought together by Mamiya's association with Mr. Honda, who is haunted by memories of the Japanese defeat at Nomonhan. Mamiya and Toru both have an affinity for being at the bottom of deep wells. Most importantly, Toru's friendship with the lieutenant is pivotal in awakening Toru's interest in Japanese World War II history.

After Kumiko leaves him, Toru begins people watching at Shinjuku station where he first encounters Nutmeg Akasaka. She and her son, Cinnamon, are involved in a secret business and eventually Toru becomes part of their organization. Going to the bottom of the well on a jinxed property eventually becomes Toru's main focus. In the well, he is able to connect with his own consciousness. In addition, he has a recurring dream about a hotel room. Toru soon discovers that he is able to pass through the wall between the well and the hotel room. After his first time going through the wall, Toru discovers a blue-black inky mark, about the size of a small child's hand, on his right cheek. There are two especially violent events in the novel that influence the main protagonist's worldview. The first involves Toru following a man carrying a guitar case. The second violent scene takes place when Toru passes through the wall into Room 208. Oddly enough, this particular violent act also brings some resolution to Toru's subconscious. Toru Okada travels through different incarnations of himself during the novel. Once, he is a young boy dreaming. In another instance, Toru is conflated with Nutmeg's father, a veterinarian at the Hsin-ching zoo bearing the same facial mark as Toru. These incarnations work with the grain of the story and reinforce the position that Toru's personality somehow fractures during the course of the narrative, only to be reintegrated at the end.