Conan runs into the black-clothed men from the pilot episode while riding the Shinkansen. He investigates further and realizes they only resemble the original two men. Using his gadget glasses and a bug, Conan overhears their conversation about a bomb in a black suitcase on board the train and is set to explode soon. Conan narrows the suspects down to four. Conan realizes a woman on the cellphone mentioned she liked viewing the mountains but her seat was facing the sea. He realizes the men's seats were facing the mountains and deduces that she was the one who met them. Conan, armed with his new power kicking shoes invented by Agasa, manages to kick the briefcase off the train before it explodes. The woman and the two men are later arrested.

Kudo Shinichi is a seventeen year-old high school detective whom people call the "Modern Sherlock Holmes." However, one night after a date with his childhood sweetheart, Ran, Shinichi witnessed an illegal trade and, caught off his guard, was knocked unconscious and fed a drug that was supposed to kill him... but he woke up and found himself shrunken to a seven year-old. In order to track down the men who did this to him, Shinichi hid his identity and lived with Ran, whose father happened to be a hopeless detective, and with that came a series of murders and mysteries that he must solve.