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.

When a car bomb goes off at a ticker-tape parade, Conan is onto one of the biggest cases of his career: a terrorist attack on Tokyo. A videotape intercepted from the crime scene may have captured the culprit's face, but while the Metropolitan Police and the Junior Detective League study the footage without success, the bombings keep escalating! And for Detective Sato, the case brings back bad memories. Can she and Conan crack the mystery before the bomber takes down the biggest target of all: Touto Tower?