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.

While wrapping up a kidnapping case, Conan and Harley find themselves on the trail of another criminal: a serial arsonist who leaves a model of a red horse at the scene of each fire. The police and fire departments are stumped, but to Conan, the case feels eerily familiar. Can he jog his memory before the arsonist claims another victim? And what will he and Harley do when Rachel and Kazuha receive the fatal red horse?