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 simple search for a missing cell phone turns into a baffling murder case. Conan has the suspects narrowed down to three reclusive eccentrics, none of whom seem upset by the victim's brutal death--and all of whom have perfect alibis. Can he solve the case by finding the phone?

Meanwhile, Rachel is convinced that Jimmy and Conan are the same person--and with Conan's cell phone, she can prove it!