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.

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.