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Shinichi Kudou, a great mystery expert at only seventeen, is already well known for having solved several challenging cases. One day, when Shinichi sees two suspicious men and decides to follow them, he inadvertently becomes witness to a disturbing illegal activity. When the men catch Shinichi, they dose him with an experimental drug formulated by their criminal organization and abandon him to die. However, to his own astonishment, Shinichi is still alive and soon wakes up, but now, he has the body of a seven-year-old, perfectly preserving his original intelligence. He hides his real identity from everyone, including his childhood friend Ran Mouri and her father, private detective Kogorou Mouri, and takes on the alias of Conan Edogawa (inspired by the mystery writers Arthur Conan Doyle and Ranpo Edogawa). Animated by TMS and adapted from the manga by Gosho Aoyama, Detective Conan follows Shinichi who, as Conan, starts secretly solving the senior Mouri's cases from behind the scenes with his still exceptional sleuthing skills, while covertly investigating the organization responsible for his current state, hoping to reverse the drug's effects someday.

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.

The series follows the adventures of Sabu, a young Edo bakufu investigator traveling with the blind master swordsman Ichi. In their travels, they assist the common people in solving mysteries and righting wrongs (usually committed by bandits or corrupt officials). Sabu is engaged to Midori, the daughter of his boss, who works as a police officer for the Tokugawa shogunate.

In the city of Judoh, Claire Leonelli has inherited leadership of the Mafia group "Vampire" following the death of his father. To keep Claire's and other criminal activities in check, the city's Bureau of Urban Safety has Special Services Division operative Daisuke Aurora and the super android codenamed "J" (whose identity is apparently kept in secrecy, as androids are banned in the city). With both of them around, crime now has little room to breathe in Judoh.