Invited for a anniversary celebration, Kindaichi, Miyuki and inspector Kenmochi re-visit the Opera House. There they discover that a play of The Phantom of the Opera is being rehearsed again. However, it doesn't take long when members of the acting troupe are killed by the Phantom. Kindaichi will once again have to solve a murder series in the Opera House.

Kindaichi, Miyuki and Fumi are invited to the resort of the Deep Blue Island by their senpai Akane, the daughter of the president of the Aizawa Group. A group of criminals infiltrate the hotel diguised as waiters to kill the members of the Aizawa Group. The criminals don't know their boss in person, and they don't know either that he's in the hotel with the members of the Aizawa Group.

Emu Hino, a 29-year-old virgin, witnesses a mob hit and fears that the killer will now find her and kill her. Indeed, he sets out to do so; he's Yo Hinomura, a talented potter and artist who's been conscripted against his will to be the prime hitman for the 108 Dragons, a gang within the Chinese Mafia, who are determined to push aside Tokyo's local crime lords. He breaks into her house, and she asks that he make love to her before he kills her; she connects to his inner self, and he becomes her protector. Now he must defend her against the local crime gang, who have connections with corrupt Tokyo police. Will Yo and Emu make it out alive, and will the 108 Dragons triumph?