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.

Flash back to one of the cases that made Jimmy Kudo famous before he became Conan! While visiting his actress mother on Broadway, Jimmy discovers some rotten apples in the Big Apple. Someone is trying to kill the stars of Golden Apple, a musical based on Greek mythology, and the only clue is a golden apple inscribed For the Fairest. While Jimmy races to crack the case, Rachel stumbles upon a mystery of her own...and a certain man in a black knit cap!