The momentous day of the opening of the new Tokyo subway, the Touto Line, has come, but a bombing incident puts all celebrations to a halt. The governor of Tokyo is caught in the blast while onboard the train, but he and everyone else present is fortunately saved by the quick thinking and actions of Conan Edogawa.

Intrigued by the incident, Conan researches the governor's political history and discovers that the man was responsible for the destruction of a village in Niigata to build the Kitanosawa Dam. Believing the attack to be related to the construction of the dam, Conan, accompanied by Ran Mouri, Kogorou Mouri, Professor Agasa, Sonoko Suzuki, and the Detective Boys, decides to visit the village and investigate.

There, they meet a group of locals who lived in the old village before it was torn down. However, just as one mystery leads to another, one of the locals is murdered. Suspecting that something much more sinister is afoot, Conan vows to uncover the truth behind these two incidents before it is too late.