Koumijima, is a beautiful island in Pacific Ocean. There is a tradition there handed down from ancient times that speaks about an ancient site under the ocean called “Sea floor Palace”, and two real pirate women, “Anne Bonney” and “Mary Lead” who left a treasure there 300 years ago.

Conan and others go to Koumijima Island on a vacation and meet with treasure hunters who have gathered there to search for the treasure, the hunters who have something suspicious about them.

One of those hunters went to search for that “Sea floor Palace”, and got attacked by a group of sharks and died.

When that happened, Conan and Haibara smelled a case behind that and started to investigate.

The legendary treasure and the murder case of the hunter are linked together with Conan deductions.
The biggest mystery: what on earth is the secret behind "Jolly Roger"?
Finally The climax scene will be transferred into "Sea floor Palace"!