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.

In a remote village, a teenage boy washes ashore with amnesia. It doesn't take long for him to be identified...as long-missing sleuth Jimmy Kudo Jimmy's friends race to restore his memory before he turns back into Conan and his secret identity is destroyed. But things go from bad to worse when Jimmy is framed for murder...