The Governor of Tokyo, Yuichiro Asakura, receives a threatening letter the day before the opening of Touto Line, a new train line for the Tokyo Metro. During the opening ceremony of the line, Conan Edogawa and the Detective Boys are driven by Professor Agasa and pass under the Touto Line. Conan, having heard about the threatening letter, notices explosives connected to the Touto railway; Using his original voice to inform the police as Shinichi Kudo, he is able to stop the train and divert traffic away from the explosives preventing any deaths.

A new member from the Black Organization that shrunk Shinichi’s body manages to find out about Shinichi’s transformation into Conan. This discovery starts to put those around him in danger as Gin and the other Black Organization members start to take action.

15 years ago, Daiichi Yachiyo Maru, a cargo ship, was crashed into a large iceberg in northern the Pacific Ocean, and sank. The captain and a crew were died. Now, in Nishitama, a ship designer of Yatsushiro Shipbuilder, which belonged to Yatsushiro Financial Combine, was suffered from a sudden hart attack while he was driving, and died in a traffic accident. Six months has passed since then. Conan, Ran, and Kogoro are enjoying their trip in the Aphrodite. The Aphrodite is a luxury liner, and it is sailing for the Pacific Ocean as its maiden voyage. However, there is a suspicious person, and finally a murder occurs. It is the beginning of a horrible plot occurred in the ocean where there is no place to escape from.

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