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.

There's always tension when Conan teams up with Harley Hartwell, the other greatest teen detective in Japan...and the only one who's still a teen! But when the duo investigates a murder at a mansion, will Conan's shrunken state interfere with Harley's detective work? And how many balconies does one mansion need, anyway? Then Conan investigates some shady doings on board an overnight passenger train. He thinks he's on top of the case...until his mystery-loving parents show up to throw everything off track!