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In spite of his new name, Conan fears the men who drugged him will discover his real identity and return to kill him and his best friend, Ran Mouri. To help counter this threat, Conan forms a Junior Detective League with his friends who wear badges as a symbol of their unity, which also double-up as walkie-talkies. However, they are often not taken seriously and as a result players must inspect every clue and possible lead thoroughly.
Players guide Conan on his quest to find clues about the origins and workings of the secret ‘Black Organisation.’ By using special gadgets such as a voice changing bow tie, players disguise Conan as Kogoro Mouri, a former police officer turned incompetent private investigator. Information gathered from the clients and cases of Kogoro must then be examined to source possible leads to infiltrate the evil group.
A breakthrough is finally made when Conan, Kogoro and Ran board a cross country train to take a break from work. Also on the train are two mysterious men dressed in black, their appearances triggering Conan’s vague memory of the night he was drugged. However, the men are carrying enough firepower to blow the train apart and so players must help Conan save the train before it’s too late.