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.

Serena's eccentric uncle has a new plan to catch the elusive Kaito Kid, baiting the master thief with a pair of priceless high-heeled shoes. The Kid is one step ahead, but with Conan on his heels he'll have to toe the line!

Meanwhile, danger lurks in Conan's own backyard. While the diminutive detective tries to crack a code found on a series of paper airplanes, he's matched deduction for deduction by the mysterious man renting Jimmy Kudo's long-vacated house. Is Subaru Okiya the mild-mannered engineering student he claims to be, or is he hiding a dark secret?