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.

Usually, Conan's mind is focused on detective work. But when Rachel falls for a handsome young doctor at a crime scene, suddenly the pint-size detective can't concentrate on the case. As Rachel threatens to give up on the perennially unavailable Jimmy Kudo, Conan starts to harbor murderous thoughts of his own...

Then the Syndicate returns! At a star-studded film festival, Conan and Anita face the shady organization that turned them into kids. But the game changes forever when one of them transforms back to the right age!