Conan, Kogoro, and Ran are out to eat at a fancy restaurant with a stream that little boats carrying food sail to the rooms they are supposed to deliver the food to. After a while three men enter the restaurant, then after eating a woman screams and Kogoro, Conan, and Ran rush to the frightened women, pointing at a dead person. How was the murder done? And why was the victim in the room he wasn't supposed to be in?

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.