Under the cover of darkness, a masked samurai murders five men across the metropolis of Japan: three in Tokyo, one in Osaka, and the last in Kyoto. In their investigation, the police learn that each man was a member of the Genjibotaru—a thieves gang centered on the theft of Buddhist statues and artifacts and who go by the names of Minomoto no Yoshitune's servants. Having received an anonymous letter containing a peculiar puzzle, the temple monks ask for his assistance in solving it to recover their long lost statue. Meanwhile, Conan Edogawa and high school detective Heiji Hattori team up in order to solve the cryptic puzzle and find the murderer, as Hattori searches for his childhood love. With Hattori's knowledge of Kyoto, the two scour the streets and gradually discover the truth.