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 Junior Detective League takes action! While playing hide and seek, first-grader Amy discovers a chopped-off head. Will Conan and friends be able to save Amy from a serial murderer?

And when Richard Moore attends a reunion of his college friends, one of them ends up with a bullet hole to her temple and a gun in her hand. Was it suicide or murder?!

Later, Conan, Richard, and Rachel attend the birthday party of the daughter of a wealthy financier. But Conan's deductive skills are put to the test when the birthday girl ends up missing and someone turns up dead.