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.

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Conan and Rachel discover that someone is posing as Detective Moore and doing good deeds...but why? A string of threatening notes left on cars gives Detective Chiba the chance to solve a case alongside his childhood crush, new police-recruit Naeko Miike. And a shocking death at a wedding party reveals a startling secret. But when Conan's investigation of the wedding leads him to an undercover detective working on the same case, he finds himself on the trail of an even bigger mystery...