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 long last, Conan has located the scientist responsible for the formula that turned him into a kid. Trouble is, she's taken the formula herself--and she can't change back! Together, Conan and the diminutive doctor track down a floppy disk that may contain the secret to curing their condition, only to find the former owner crushed under a fallen bookshelf. Can they crack both the locked-room mystery and the locked disk?