Shuuhei Sazaka is a young boy who loves playing hide-and-seek. One day, he decides to play the game with his longtime friend Kaori, letting her be the one to hide. However, the fun stops abruptly when Kaori cannot be found and is thereafter never seen again. Throughout the next eight years, Shuuhei resents himself for never being able to find her.

As time passes, strange "mazes" start appearing, seemingly at random. Blamed for the increasing cases of disappearances over the past years, these mazes are eventually discovered by Shuuhei himself. Unexpectedly, Shuuhei meets Kaori in one of the mazes, but she is no longer the girl he once knew.

Nemuri no Fuchi follows Shuuhei as he tries to unravel the mystery behind the connection between the mazes and those who disappear.