The Governor of Tokyo, Yuichiro Asakura, receives a threatening letter the day before the opening of Tohto Line, a new train line for the Tokyo Metro. During the opening ceremony of the line, Conan Edogawa and the Detective Boys are driven by Professor Agasa and pass under the Tohto Line. Conan, having heard about the threatening letter, notices explosives connected to the Tohto railway. Using his original voice to inform the police as Shinichi Kudo, he is able to stop the train and divert traffic away from the explosives preventing any deaths.
Conan researches Asakura's political history for a clue on the culprit and learns that the governor was in charge of the construction of dam in Kitanosawa, a fictional town in the Niigata Prefecture. Due to the dam's construction, the citizens of Kitanosawa were forced into a new town and their old homes were drowned by the dam. Since Asakura's trip to celebrate the anniversary of the dam is canceled by the bombing, Conan speculates information on the bomber could be found in Kitanosawa and plans a trip there.
Conan, the Detective Boys, Ran Mouri, Kogoro Mouri, and Sonoko Suzuki travel to Kitanosawa and enjoy the day playing. They are introduced to a group of locals; their names are Keisuke Yamao, Mizuki Tono, Fuyumi Tachihara, Takehiki Muto, and Shogo Hikawa. The group reveals they were all childhood friends and were part of the group which relocated to the new village. They also reveal its their first gathering in eight years since Yamao was in prison for killing Tono's sister, Natsuki Tono, in a hit and run.
Hit and Run (Past)
Way to Kitanosawa Village
Cause of death:
Hit by a car
On the way to Kitanosawa Village, Yamao got into accident with Natsuki Tono, Mizuki's younger sister, and killed her as result.
The next day, Tachihara's son, Touma Tachihara, awakens from his eight year coma with no memory of his accident. Later that day, Hikawa is found dead in a field.
Snowy field in Kitanosawa
Cause of death:
Keisuke Yamao, Mizuki Tono, Fuyumi Tachihara, and Takehiko Muto
Originally, it was assumed to be suicide since only Hikawa's footprints were found in the snow. Conan reveals Hikawa was killed by an electroshock weapon. The culprit then waited for it to snow and walked away backwards to suggest Hikawa was alone. During a diamond dust caused by the sunrise, Touma experiences a flashback on the day of the accident.
Conan investigates Hikawa's belongings and finds a newspaper clipping detailing a jewelry store was robbed the day before the hit and run.
Robbery - Murder (Past)
Cause of death:
On the 15th at around 11:00 pm. An unknown perpetrator broke into Misuzu Jewelry located at Yaoi City, Shinjuku Ward, Tokyo. And stabbed 51-year-old company president Misuzu Eiko to death with a sharp blade. The robber allegedly made off with one billion yen worth of jewelry.
A cell site is destroyed by bombs leading Conan to hypothesize who the culprit possibly is. Meanwhile, the Detective Boys and Touma are hunted down by a sniper.
Conan intervenes and leads them to safety. Taking a route towards the dam, Conan explains Keisuke Yamao is the culprit. Yamao robbed the jewelry store in a distant town and drives back to Kitanosawa. On the way, he runs over Natsuki, a scene which Touma notices. Touma is then kidnapped by Yamao and sees the diamonds, explaining why the diamond dust startled his memories. Touma escapes but falls down a cliff leading to his coma. Yamao then buries the jewels in a property in Kitanosawa and turns himself over to the authorities for Natsuki's death. Unexpectedly, the dam project forced the town of Kitanosawa underwater. As a result, Yamao decides to bomb the dam to search old-Kitanosawa for the diamonds. In order to have enough time to perform the search, he had to cancel the Governor's trip and destroy the cell site to prevent the outside world from learning off the dam's destruction.
Upon arriving at the dam, Conan is pursued by Yamao who tortured him and intends to kill him. Yamao is then shot and incapacitated by Mizuki. Touma regains his memories of the accident upon seeing Mizuki and reveals he saw Mizuki push Natsuki off into the road. Mizuki professes she was the sniper attempting to kill Touma and that the death of her sister was an accident. Yamao, having set off the bombs in the dam forces them to flee. Conan diverges from the group intending to start an avalanche by creating grooves in a steep mountain with his motorized snowboard to divert the flow away from Kitanosawa. He is successful but his motor short-circuits causing him to be caught in the avalanche. He is eventually freed when Ran calls Shinichi's cellphone causing him to regain consciousness to alert the others of his position.
The largest arch dam with discharges at the center of the body and spillways in the opening scenes of the end credits is the Kurobe Dam, which is located in Toyama Prefecture and is currently the highest dam in Japan. It was designed and built by Carlo Semenza along with his deputy Alberico Biadene, the two Italian engineers who were involved in the Vajont dam disaster.