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.

Kir, a captured agent of the Men in Black, lies comatose in a hospital, her location a matter of international security. When the Men in Black discover her whereabouts, Conan needs help from the professionals. Time for the pint-size detective to team up with the FBI! Conan, Agent Starling and the mysterious Agent Arakai hatch a plan to transport Kir to a safe location. But can they stay one step ahead as the Men in Black descend on Tokyo and the Metropolitan Police join the fray? The biggest, most explosive, most game-changing case in Conan's career is underway!