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 Kaito Kid has vowed to steal a famous artist's latest painting - and Conan is on the scene! But while Conan prepares to stop the theft, a man is killed right under his nose. Is the Kid the culprit?

Then, a small boy is the only witness to a murder, but no one can make heads or tails of his strange testimony. And Conan is distracted by his suspicions of Rachel's new friend Eisuke, who bears an eerie resemblance to one of the agents of the Men in Black!