During the inauguration of Tokyo's new Touto subway line, a bombing occurs, injuring the city's governor who was on board the train. Thanks to Conan Edogawa's quick actions, the governor and other passengers are saved.
Driven by curiosity about the bombing, Conan investigates the governor's political history and discovers that the governor was involved in demolishing a village in Niigata for the construction of the Kitanosawa Dam. Believing the bombing is linked to this past event, Conan, along with Ran Mouri, Kogorou Mouri, Professor Agasa, Sonoko Suzuki, and the Detective Boys, travels to the old village to further investigate.
Upon arrival, they meet some of the former villagers. However, another mystery unfolds when one of these individuals is found dead. Conan, now convinced that a more sinister plot is at play, is determined to uncover the truth behind both the bombing and the murder before it's too late.