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Child prodigy Hiroki Sawada—who, by the age of ten, is already a MIT grad student and has developed a DNA Tracker software—has been under the guardianship of Thomas Schindler, owner of the software giant Schindler, Inc., since his mother died. One night, in a heavily guarded room at the top of the Schindler building where Hiroki lives, he finishes an artificial intelligence system, Noah’s Ark, and sends the software through the telephone lines. The guards become suspicious and try to enter his room. They discover that Hiroki leapt off the building to his death.
Two years later, at the Beika City Hall, Schindler, Inc., holds a demonstration of a virtual reality game called Cocoon. The Detective Boys are invited to the demonstration but cannot participate without special badges. Doctor Agasa and Booker Kudo arrive at the City Hall. Agasa gives Conan Edogawa a badge, and the other Detective Boys exchanging Premium Golden Yaiber Cards for badges. They all use the badges and participate in the demo.
In another room, Conan discovers the corpse of Kashimura, a top employee of Schindler, Inc., and his dying message on a keyboard: J-T-R. He decides to participate in the demonstration, hoping that the game would lead him to an answer. Booker finds out that J-T-R stands for “Jack The Ripper”.
When the demonstration begins, Hiroki’s artificial intelligence system, Noah’s Ark, takes control of the game system Cocoon. It tells the audience that if all fifty kids in the demonstration lose the game, it will kill the kids with a large electromagnetic burst. The kids in the demonstration are given a choice of five stages in the game, and Conan and the Detective Boys choose the fifth, a re-creation of a 19th century London mystery. Conan and his friends track down 221B Baker Street, only to find that Sherlock Holmes and Dr. Watson are at Dartmoor. Since Holmes cannot help, the kids find Sebastian Moran and Professor Moriarty. Moriarty tells Conan that he trained Jack the Ripper when Jack was a street urchin. The professor gives the children a clue about the next victim, who turns out to be Irene Adler, Holmes’s only love.
In the real world, Booker investigates the case. Booker reveals that the murderer is the company’s president, Thomas Schindler. Schindler is a descendant of Jack the Ripper who will stop at nothing to hide his secret. Schindler is immediately arrested.
One by one, the children “die,” until only three are left: Conan, Rachel Moore, and another child, Hideki Moroboshi. They follow Jack the Ripper to a runaway train, and the murderer leads them to the top of the train. There, Jack the Ripper ties himself to Rachel and threatens Conan. To save Conan, Rachel sacrifices herself by jumping off the train and into a ravine, taking the Ripper with her. As Conan begins to lose hope, Sherlock Holmes appears and gives Conan some useful advice that eventually helps Conan and Hideki survive the game. After winning the game, Conan reveals that Hideki is actually the Ark in disguise. All the children are released from the demonstration, and the Noah’s Ark destroys itself.