Conan and his friends were invited to the premier of an new virtual computer game. But someone programmed the game, that if they can't answer the riddle in the game, they all have to die.
Hiroki Sawada was a 10-age kid who got into a US college and even graduated. One day, Hiroki finished A.I. Noah-sue-ark and suicide to end his life. 2 years later. Conan and Rachel and Genta,Ayumi,Mitsuhiko,Haibara finally able to play Cocoon but Noah-Sue-Ark modified the program and made Cocoon more and more harsh and difficult with these 5 scenes: Viking. Paris Dakari Race. Colosseum. Solomen Treasures. 1888 London. The condition the Noah Ark altered was the 50 kids must be able to have one survived or else none of them can survive in real world if all got killed. Which scenario would Conan choose, and what would happen?—Kazuha
Child prodigy Hiroki Sawada is introduced by a TV program running in the background, while Hiroki himself is working on a computer. The program host explains that by the age of ten, he is already a MIT graduate school student and has developed a DNA Tracker software and is now in the final stage of his second major project, an artificial brain dubbed Noah's Ark. The program host goes on to explain that Hiroki has been under the guardianship of Thomas Schindler, owner of the software giant Schindler, Inc., since his mother died, and that he has been put under a rigorous study program and has had a somewhat deprived childhood. After turning the TV off, Hiroki finishes Noah's Ark, and sends the software through the telephone lines, which causes his computer to show the message "Noah's Ark Sailed Out", simultaneously triggering an alarm in the guardroom. The security guard calls Thomas Schindler and both try to enter Hiroki's room. When they finally break into Hiroki's room, they find that Hiroki is not in the room. Schindler finds Hiroki's shoes on the balcony; He jumped from the top of the building to his death.
The image on his computer screen shows an ark sailing in water and the words "Good-bye Hiroki."
Two years later, at the Beika City Hall, Schindler, Inc. holds a demonstration of a virtual reality game system called Cocoon. Many kids, including the Detective Boys, are invited to the demonstration. However, only the kids with badges are chosen for the demonstration. Professor Agasa and Yusaku Kudo arrive at the City Hall. Agasa gives Conan Edogawa a badge and tells Conan that his mother, Yukiko Kudo, would not be there because of an alumni reunion. The rest of Detective Boys trick a few kids by exchanging badges for the Premium Golden Yaiba Cards. They all use the badges and participate in the demonstration.
In another room, Schindler kills Kashimura, one of his top employees, and Kashimura types in a dying message: the letters J, T and R. Conan discovers the murder and decides to participate in the demonstration, hoping that the game would lead him to an answer. Yusaku, having worked with Kashimaru on the game, recognizes 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. When two of the parents try to get the children out, the parents get shocked by a sudden burst of electricity. Noah's Ark then warns 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 final stage, a re-creation of an 1800 London mystery. In the beginning of the game, Conan discovers that Agasa's inventions don't work. After receiving a hint from Prof.Agasa they decide to go to Sherlock Holmes for help. As they near 221B Baker Street they meet a strange accordion playing vagrant who sings a strange song, but they shrug it off. Conan and his friends arrive at 221b Baker Street, only to find that Holmes and Watson are at Dartmoor. Mistaken for the Baker Street Irregulars by Mrs Hudson, they are invited inside. Ran finds Sherlock's investigation notes on Jack the Ripper, which implies that Jack is highly likely to have a connection to Professor Moriarty. Since finding the Professor is next to impossible, the kids decide to talk to his right hand man Colonel Moran at his favorite hang-out to find out the Professor's location. After causing a brawl and losing Mitsuhiko, Ayumi and Genta, Conan forces the Colonel into a standoff by holding Moriarty's wine hostage. It is at this moment an elderly gentleman comes and announces that Professor Moriarty requests an audience with the group. After being led to another gentleman in a carriage, Conan calls out Moriarty for testing them; Moriarty was the gentleman who led them there. After explaining their situation, Moriarty reveals that he found and trained Jack the Ripper when Jack was a street urchin. The professor promises the children an opportunity to bring Jack down by posting a message in the next day's newspaper to kill someone, but refuses to name the victim-to-be, telling them they'd find out by reading the paper. The next day after reading the paper they realize the next victim is to be Irene Adler, the only woman Holmes ever loved.
It is revealed by Yusaku that while he and Tadaaki Kashimura were both college friends and partners in developing the game, he was also employed by Kashimura as a detective to investigate the motive behind Hiroki Sawada's suicide. Yusaku also reveals Kashimura was Hiroki's real father. In the real world, Yusaku continues to reveal the truth behind the case. Yusaku reveals that the murderer is the company's president, Thomas Schindler. Schindler is revealed to also be responsible for Hiroki's suicide. Hiroki discovered the DNA of Jack's second victim on a dagger purported to have belonged to Jack himself through his DNA searching program. Schindler realized that it was only a matter of time before Hiroki would consequently discover that Jack's blood now runs through Schindler himself. Schindler then proceeded to isolate and pressure Hiroki further, ultimately leading to Hiroki's suicide. Kashimura was killed because Noah's Ark gave that same data to Kashimura. Schindler is immediately arrested.
While protecting Irene Adler two more children are lost. Ai also loses while protecting Conan, leaving only three: Conan, Ran and another child, Hideki Moroboshi. They follow Jack the Ripper to a runaway train, where he dons a disguise and merges with the passengers. Conan correctly deduces which one of the passengers Jack is disguised through the use of Sherlock's notes. After being revealed. Jack throws a smoke bomb while Ran charges him. When the smoke clears Conan and Moroboshi find that everyone is gone. Traveling to the engine room they find that there is no driver and that the train is speeding out of control, with the brakes destroyed. Conan discovers Jack and Ran on the top of the train. There, Jack the Ripper reveals that he has tied himself to Ran and threatens Conan. Ran decides to save Conan and sacrifices herself by jumping off the train and into a ravine, taking Jack the Ripper with her. As Conan begins to lose hope, the mysterious vagrant, who is actually 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 Moroboshi is actually the deceased Hiroki Sawada (in the form of the Ark) in disguise. They chat a little and before saying goodbye to Conan, Hiroki reveals to him that he knows the detective's identity as Shinichi Kudo. After that, the Noah's Ark destroys itself. All the children, including Ran and the Detective Boys, are released from the cocoons. Yusaku then congratulates Conan for beating the game.
