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.

In yet another scheme to get her estranged parents back together, Rachel arranges a luxury hotel getaway. But rest and relaxation are off the schedule when a corpse turns up in the bedroom. Then the Junior Detective League is enlisted to protect a priceless statue from the Kaito Kid's thievery. The kids are sure it'll be a breeze...until they have to solve the case without Conan!