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.

Doc Agasa takes Conan and his young Junior Detective League pals to an old, abandoned mansion for a treasure hunt. When the pint-size investigators find a mysterious box, they open it and discover it is full of smashed toys and a violently stabbed teddy bear! Conan follows the trail of clues and runs smack-dab into a dead old man in an attic! Who killed the old man, and more importantly, who killed teddy?