The series depicts the cases of a young private detective who was inadvertently turned into a prepubescent boy by a certain criminal organization. Even with his body shrunk, he continues to solve many cases and is struggling to solve the mysteries of the criminal organization responsible in order to return to his normal body.
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The story starts by introducing 17-year old (initially 16 years in the manga) high school student Kudo Shinichi who is a genius savant, and his childhood friend and crush, Mouri Ran. Shinichi treats Ran to a trip to a theme park named "Tropical Land" and encounters a roller coaster murder case. After easily solving the case and showing off his detective skills, he notices two mysterious men wearing black. Telling Ran to go home, he tracked the men to a meeting place and witnesses an illegal deal. However, one of the men in black (known only as Gin) notices him and knocks him out. Instead of directly killing him, the two men in black give him an untested experimental poison named Apotoxin-4869 (APTX4869), which was supposed to not only kill Shinichi, but also leave no traces of poison in Shinichi's body. However, Shinichi wakes to find himself alive and shrunken to a six-year-old Shinichi.

Following the advice of Proffessor Hiroshi Agasa, Shinichi hides his real identity, lest the men in black find out that he is alive. When Ran asks for his name, Shinichi spots books by Arthur Conan Doyle and Edogawa Rampo and comes up with the name "Conan Edogawa". Agasa says that "Conan" is a relative of his, but that he is too busy to take care of a young child, and suggests that Conan go to live with Ran, and both Conan and Ran agrees. Conan feels that by living with a detective, he may be able to amass clues that would lead him to the people who poisoned him.
However, Ran's father, Mouri Kogoro is an inept detective and Conan always solves mysteries in his stead, while he gets the credit. As Conan appears to be just a boy, police do not pay any attention to him. Conan instead uses Detective Kogoro by putting him to sleep with an "anesthesia gun-watch" and pretending to be Kogoro by using a voice changer disguised as a bow tie. These gadgets and more are made by Dr. Agasa.
To maintain his cover, Conan goes to Teitan Elementary School and has made friends with three children at the school, Genta Kojima, Mitsuhiko Tsuburaya, Ayumi Yoshida who formed the self-styled "Junior Detective League". Although Conan feels profoundly self conscious playing with them given his true age, the foursome have numerous adventures of their own and the trio have proved capable assistants to the detective for their age.
Shinichi was able to find out that Gin was working for a huge international crime syndicate, known as the Black Organization. In addition to Gin, other major members and operatives of the Black Organization that appear later in the story include his partner Vodka, Vermouth, Kir, Chianti, Korn, and a mysterious "boss" who has only been mentioned so far. Shinichi also meets the inventor of the APTX4869 and former member of the organization, Shiho Miyano (codename "Sherry" within the black organization), who was also turned into a child after she took her own drug in order to escape the organization. She later lives with Dr. Agasa under her new alias, Ai Haibara.
Later in the series, Shinichi meets with his parents, Kudo Yusaku and Kudo Yukiko, along with Heiji Hattori, a rival detective from Osaka who later becomes his good friend, and Heiji's childhood playmate, Kazuha Toyama. Another recurring character is the gentleman thief known as the Phantom Thief Kid (Kaito Kid). Aside from the Black Organization members, he is the only person that Conan seems unable to catch, and neither realize that they are both after the same bad guys for different reasons.