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The compilation film recompiles the anime's "Jet-Black Mystery Train" arc, while also including key scenes centering on the character Ai Haibara from other parts of the television anime's run, as well as new footage connecting the film to Detective Conan: Kurogane no Submarine at the end of the film.
Kogoro Mori, private investigator extraordinaire, is behind bars! The well-liked but bumbling P.I. is linked to a mysterious explosion at Edge of Ocean, Tokyo’s new cutting-edge technology district, and the proposed site of the international Tokyo Summit. Enter Shinichi Kudo, master detective, who still suffers from an age-reversing drug and masquerades as the much smaller master detective, Conan Edogawa! Conan is intent on solving the case and freeing the father of his dear friend Ran, but as he uncovers a mysterious suicide and encounters some puzzling friction between two of Japan’s law enforcement agencies, seemingly every single internet-connected device in Tokyo, all the way up to washing machines and cars, suddenly malfunctions. A dangerous hacker is afield, pushing a deadly grudge, and to catch them Conan will need to enlist the help of the secret head of Japan’s Public Security Division: Zero, the Enforcer!
Between August and October, 1952, a series of unusual crimes takes place in Musashino and Mitaka: the attempted murder of 14-year-old Kanako Yuzuki, Kanako's abduction from the strange research "hospital" where she was recovering, then abductions of other girls, followed by their severed limbs in custom-fitted boxes being placed in surrounding towns. News editor Morihiko Toriguchi and crime fiction writer Tatsumi Sekiguchi investigate with the help of onmyōji Akihiko Chūzenji.
Follows Kimihiko Kimitsuka, a young man who four years ago became the assistant of a mysterious detective known as "Siesta" on a hijacked airplane. Together, Kimihiko and Siesta went on mind-boggling, globe-trotting adventures while combatting a secret organization, but all of that came to an end when they were separated by Siesta's death. In the present day, Kimihiko tries to return to an ordinary, boring life as a high school student, but things are never that simple, even though the detective is already dead.