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.

A wealthy woman with a clock obsession is murdered after receiving a threat from the Guardian of Time. What is the secret of the old clock? Can Conan make a timely arrest?

Then Conan takes on a dangerously tasty case at a noodle shop where the specialty of the house is Ramen to Die For. And at the scene of a murder, Conan and Rachel meet a teen detective who matches them at sleuthing and martial arts!