Jimmy Kudo, the son of a world-renowned mystery writer, is a high school detective who has cracked the most baffling of cases. One day while on a date with his childhood friend Rachel Moore, Jimmy observes a pair of men in black involved in some shady business. The men capture Jimmy and give him a poisonous substance to rub out their witness. But instead of killing him, it turns him into a little kid! Jimmy takes on the pseudonym Conan Edogawa and continues to solve all the difficult cases that come his way. All the while, he's looking for the men in black and the mysterious organization they're with in order to find a cure for his miniature malady.

A man is found beaten senseless in a parking lot, and the criminal he fingers is...George? Time for the Junior Detective League to spring into action and clear their friend's name! Then a discovery in the school library reminds Conan of one of his first cases. Flash back to the young Jimmy and Rachel as they track down a sinister intruder in their elementary school after dark...an intruder who seems to have supernatural powers! Can two ordinary kids solve a code left by a master of mysteries?