After escaping from well-meaning but skeptical park security, with nowhere else to go Shinichi runs home. He there encounters into his next door neighbor and close family friend, Professor Agasa. He convinces Agasa of his identity and head inside Shinichi's home to discuss the next move. Agasa warns him that he must keep his identity secret because the Black Organization will kill him and others associated with him should they discover the truth.

Ran arrives to find out what happened to Shinichi, which forces him to come up with the alias Conan Edogawa from Arthur Conan Doyle and Rampo Edogawa and he pretends to be a distant relative of Agasa's, who places Conan in Ran's care. Ran's father Kogoro Mouriowns a Detective Agency, which will allow Conan to run into cases involving the Black Organization. He occasionally uses Kogoro, and Agasa, among others as a mouthpiece to solve crimes while searching for how to get his body back.

In the meantime, to protect his identity he is forced to play the part of a first-year Elementary student, enrolling as a student at Teitan Elementary. Three of his classmates, Ayumi, Genta, and Mitsuhiko, befriend him and pull him into creating the Detective Boys,  after which he tries to keep them out of trouble. Their group is later joined by the creator of APTX 4869, Shiho Miyano, shrunk down and using the alias Ai Haibara.

Although he mostly uses the Conan alias to solve cases, in some (especially emergency) situations, he uses the Voice-Changing Bowtie to call the police using his original, Shinichi's voice and get involved with cases, which allow him to gain the authority that Conan lacks. In the aftermath; however, Shinichi requests his identity not to be revealed to the public, a clear contrast to what his attention-seeking behavior before turning to Conan.