Ran and Sonoko are off to see a concert sang by TWO-MIX. Meanwhile, Conan and the Detective Boys accidentally bumps into one of the singers for TWO-MIX, Minami. Minami takes the Detective Boys out to eat lunch then she gets up to take a phone call and gets kidnapped by two men. In the car was also the other member of TWO-MIX who was also kidnapped. The Detective Boys report it to Megure and then the kidnapper calls.

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.