It has been three days that Shinichi has been shrunk and stays at Ran's place. Conan then goes to school, where he meets three of his classmates, Ayumi, Genta and Mitsuhiko that wants to be friends with him. After school, Conan visits Professor Agasa, which give him a new gadget. On his way to the Detective Agency, he is staring at Kogoro because he was useless for him to find the men in black. A car then stops in front of the agency, and the three classmates of Conan are spying on him. Kogorō later got a customer, but doesn't show any interest unless he noticed it was Yoko Okino which Kogorō changes himself quickly. Yōko tells that she has been staled for three days, which that Kogoro and the others are going to her apartment to figure out who. Ones arrived at her apartment, they see a dead body on the ground with a knife on his back. Later it has been known that it is a murder case, Yōko and her manager Yamagishi where both suspects on the murder case, which later a third suspect has been added, Yōko's rival Yūko Ikezawa. The case later has been closed, containing that it was suicide and the dead person contains to be Yōko's ex-boyfriend Akiyoshi Fujie.

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.