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.

When a master magician commits suicide his wife suspects foul play and pays a visit to private detective Richard Moore's office. The culprit is one of the dead magician's three assistants. Can Conan find out which one of them had something deadly up their sleeve? Plus, Rachel takes Conan's glasses off while he is sleeping and discovers Conan looks just like a young Jimmy Kudo! Is Jimmy's cover blown? Or can he find a way to pull the wool over her eyes yet again?