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.

Stranded in the woods, Conan and his friends take shelter at a spooky old house - only to witness a seemingly supernatural murder. The knife-wielding old lady who lives there couldn't be a witch...could she? Then Conan finds a lead in his ongoing investigation of Eisuke, Rachel's suspicious new friend. But by the time he chases it down, the source is dead and the information is missing. To get the facts, Conan has to solve the crime!