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.

At a mystery-themed college party, a fire threatens the life of a pretty freshman--and Conan suspects arson. But Rachel is more worried by the discovery that the victim has a past with Jimmy Kudo. Can she compete with Jimmy's beautiful, brilliant first love? Then the Junior Detective League stumbles upon a counterfeiting operation led by a woman in black, and Conan finds himself on the trail of the shadowy crime syndicate that turned him into a kid--not to mention the scientist who created the de-aging formula!