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.

Surely the Junior Detective League can't get into any trouble at an afternoon monster movie. But when a man in the audience dies, Conan and Anita realize that the real monster isn't the big green behemoth on the screen. Then Rachel gets her own movie moment, playing Rose--minus Jack--at the prow of a glittering ocean liner. When a suspicious explosion kills the romance, it's time for Conan and teen detective Harley Hartwell to make sure that the passengers' hearts will go on!