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.

It started as a simple case: find a missing computer programmer suspected of scamming his clients. But when Detective Moore finds his man, Conan finds something else--evidence of the elusive Men in Black! Can an abandoned diary put Conan on the trail of the criminal syndicate that de-aged him? What clues are coded into the go board the computer genius left behind? For the first time, Conan gets close to the Black Organization--too close for comfort!