The story follows about a boy named as Shinichi Kudō that solved a case at a mansion. The next day, on his way to school, his case was all over the news and was being satisfied by that. His best friend Ran Mōri later showed up walking their way to school. At school, Ran remembers what Shinichi promised her, but seems to have forgotten. Shinichi does remember it later, which on the next day, the two went to Tropical Land, a theme park located in Beika City. There a man has been decapitated while they where in the roller coaster. Shinichi solved the case, which after solving the case, he is following one of the suspicious men that he has seen on the roller coaster. There he finds a shocking discovery, but didn't noticed his partner which Shinichi has been smacked unconscious. The man in black gives Shinichi a poison which turns his body into a elementary kid.

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.