Bombing case at Nichiuri TV in autumn. The Satsuki Cup, which crowns the winner of Japan's Hyakunin Isshu, is currently being filmed inside the facility. The incident results in a big commotion and, while the building is burning to ashes, the only people left inside are Hattori and Toyama Kazuha. They get rescued just in time by Conan , who rushes to the scene. Both the identity and purposes of the bomber are unknown.
A new member from the Black Organization that shrunk Shinichi's body manages to find out about Shinichi's transformation into Conan. This discovery starts to put those around him in danger as Gin and the other Black Organization members start to take action.
Mouri Kogoro is called to a special case in the ancient capital of Kyoto. There, Conan meets Heiji and they team up once again to solve the case, recover the stolen Healing Buddha statue, and even discover the identity of Heiji's first love.
As a pair of towers in Tokyo are being prepared for their grand opening, there is a series of murders of people connected to the towers. Conan suspects that the mysterious Syndicate may also be involved.