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As a pair of towers in Tokyo are being prepared for their grand opening, there is a series of murders of people connected to the towers. Conan suspects that the mysterious Syndicate may also be involved.

While visiting Hachijo-jima, Conan sneaks aboard a security boat heading to the Pacific Buoy, an off-shore facility constructed near the coasts built to connect surveillance cameras used by police forces around the world. However, an engineer gets abducted! An eerie sound of a propeller hums underwater as a dark figure begins to creep toward Ai Haibara... When the forbidden Black Box is opened, the sealed-away past will surface above the treacherous waves!

In the aftermath of her husband's death, widow Ramona's struggle to raise her two kids is hindered by the arrival of a mysterious woman with supernatural abilities.