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.

A mysterious letter brings Conan and his friends to a mansion full of beautiful clocks that aren't quite behaving themselves. As Conan attempts to figure out what's wrong with the timepieces and who wrote the letter, he uncovers a tale of treasure, thieves and a family tree with very twisted branches. Plus, a famous actor's wife meets with an unfortunate accident right in front of Conan, who takes on the mission to find out about her sudden demise.