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.

When Richard Moore flubs a ten-million-yen case, two women step in to save the day: Eva Kaden, crack attorney and Richard's ex-wife, and Vivian Kudo, brilliant actress and Jimmy Kudo's mom! But the brainy blond duo is up against a killer who can go anywhere without being seen! Meanwhile, shadowy figures are trailing Anita and Conan, and ditzy American teacher Miss Jodie seems to know far more than she pretends. Have the Men in Black finally caught up to the shrunken sleuth?