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 meets his trickiest adversary yet when the Sebastian Financial Group hosts an exclusive party on the lavish ocean liner the Q. Selizabeth. All 500 guests are wearing a copy of the priceless jewel the Black Star pearl. One pearl is the real thing. And one guest is also the notorious thief Kaito Kid, aka Phantom Thief 1412, who is bent on leaving the event with one very expensive party favor. Can Conan save Serena's family heirloom from a master thief who's also a master of disguise?