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.

During a school field trip, Conan and Rachel end up in a mountain cabin with several members of the teaching staff. Conan gets quite a surprise when he answers the doorbell and a frozen teacher's corpse falls into the house! To add to the mystery, a strange letter is written on the teacher's hand, which sends another of the educators running to his room. Shortly after, he's found dead too! Can Conan put his brainpower to work and solve the mystery before the students run out of teachers?