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.

On the trail of a gang of bank robbers, Agent Starling teams up with the Junior Detective League. But she finds more than she expected when she uncovers evidence that Agent Akai, believed to have been assassinated by the Men in Black, may be alive!

Then Mr. Moore is summoned to a mansion to investigate a strange murder, only to find that the killer isn't finished. Why were five gifted people invited to live in the mansion, and what is the secret of the Red Wall?