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.

The Metropolitan Police investigate a stalking case that turns into murder...and Detective Santos feels a strange connection to the victim's girlfriend. Could she be his half-remembered first love, a girl who loved cherry blossoms? Or is she the killer?

Then the Detective League investigates a haunted warehouse with a treasure-eating monster. And Harley Hartwell enlists Conan's help to retrieve his lost lucky charm, only to not-so-luckily stumble upon a crime!