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.

Alone at the detective agency, Rachel and Serena face off against a bomber with a bizarre demand. Conan and the Junior Detective League race to rescue Doc Agatha from kidnappers with an unexpected target. And Harley and Kazuha visit Conan and Rachel in Tokyo, only to get caught up in a case that may solve the eternal question: who's the greatest teen detective team?