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 Men in Black are back--and they've got a political candidate in their crosshairs! After eavesdropping on their plans, Conan teams up with the FBI to stop the assassination. But if the Men in Black realize they've been bugged, their next target will be Richard Moore's home!

Can Conan save the politician without putting Mr. Moore and Rachel in danger? Only if he can decipher the code words the Men in Black use to plan their hit!