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.

When Conan and Harley join forces to win a crime-solving competition, it's not all fun and games. The head of a toy company has been murdered, and the only clue is a cryptic message spelled out in wooden blocks. Then the detectives race to find a terrorist at a baseball championship--and with a bomb planted somewhere in the stadium, they can't afford to strike out Meanwhile, Anita makes a difficult choice. Given the opportunity to enter the Witness Protection Program, will she disappear from Conan's life forever?