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.

Conan and his friends take a well-deserved break at a video arcade--until one unlucky gamer is found dead in the seat of a virtual-reality game. As Conan and Rachel investigate, they're joined by an unlikely new accomplice: Rachel's English teacher, Ms. Saintemillion. Outside the classroom, the fast-talking American turns out to have an itchy trigger finger--at least when it comes to video games--and a suspiciously keen interest in Conan. Has the shrunken sleuth stumbled upon a valuable new ally...or an enemy agent?