Kafka on the Shore contains several riddles, but there aren't any solutions provided. Instead, several of these riddles combine, and through their interaction the possibility of a solution takes shape. And the form this solution takes will be different for each reader. To put it another way, the riddles function as part of the solution.

Comprising two distinct but interrelated plots, the narrative runs back and forth between both plots, taking up each plotline in alternating chapters. The odd-numbered chapters tell the 15-year-old Kafka’s story as he runs away from his father's house to escape an Oedipal curse and to embark upon a quest to find his mother and sister. After a series of adventures, he finds shelter in a quiet, private library in Takamatsu, run by the distant and aloof Miss Saeki and the intelligent and more welcoming Oshima. There he spends his days reading the unabridged Richard Francis Burton translation of One Thousand and One Nights and the collected works of Natsume Soseki until the police begin inquiring after him in connection with a brutal murder.

The even-numbered chapters tell Nakata's story. Due to his uncanny abilities, he has found part-time work in his old age as a finder of lost cats. The case of one particular lost cat puts him on a path that ultimately takes him far away from his home, ending up on the road for the first time in his life. He befriends a truck driver named Hoshino, who takes him on as a passenger in his truck and soon becomes very attached to the old man.