The story takes place off the coast of Hachijojima, Tokyo, where a marine facility called "Pacific Buoy" has been built, which connects police surveillance cameras from all over the world. Before the facility was officially launched, IT engineers from all over the world came to the site to connect to the jurisdiction of Europol. At the same time, a test of a "new technology" that uses a facial recognition system is also underway... On the other hand, Conan and the Junior Detective Team came to Hachijojima to watch whales at the invitation of Sonoko. At this time, Conan received a call from Okiya (Akai Shuichi) and was told that a member of Europol was killed by Gin in Germany. In order to investigate the truth, Conan sneaked into the security boat of Metropolitan Police Department personnel such as Kuroda Heibei who went to the "Pacific Buoy" for security work and entered the facility. Later, in the facility where preparations for the system launch were steadily underway, a case occurred-a female engineer was kidnapped by the Black Organization, and the USB flash drive containing certain information in her hand also fell into the hands of the Black Organization. A creepy propeller sound came from the sea. At this time, a dark shadow was approaching Haibara Ai on Hachijo Island...