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.

[Written by MAL Rewrite]

In Touto Stadium, a J. League soccer match is taking place. During this, Detective Kogorou Mouri receives a bomb threat from an unknown caller and a mysterious riddle that points to its location. Conan Edogawa must now save the fans of the game before the time runs out.

Fortunately, with Conan's quick actions and clever thinking, the bomb is discovered and the explosion is evaded. The culprit does not stop there; Detective Kogorou is informed of another hidden bomb set to explode at a large event in the city. Forced into a race against time, with thousands of more lives at stake, Conan must decipher another riddle, discover the place of the bomb, and catch the culprit in order to escape a terrible tragedy.

[Written by MAL Rewrite]

The warship Aegis Destroyer is conducting public exercises in Maizuru Bay where, coincidentally, a suspicious foreign ship was recently spotted. Conan Edogawa, Ran Mouri, Kogorou Mouri, Sonoko Suzuki, and the Detective Boys all receive a ticket to attend this event. However, while the ongoing military operations are underway, one of the crew members comes across a lieutenant's severed left arm. Conan later discovers that a foreign spy may have infiltrated the warship to obtain classified information by any means necessary. If the information were to leak, Japan's line of defense would be exposed, leaving the country unprotected from hostile attack.

With the help of the police at sea while other friends and allies investigate on the mainland, Conan must now prevent this national crisis and identify the spy for the sake of Japan.

[Written by MAL Rewrite]

One morning, at the observation deck of the Bell Tree Tower, a man is suddenly shot dead by an unknown sniper. Conan Edogawa, who happened to be visiting as the murder occurred, rushes to apprehend the sniper but fails to do so. He later learns that the suspect for the incident, Timothy Hunter, is a former member of the Navy Special Ops squad and was already being investigated for a previous murder case. The FBI believes that there are at least three people Timothy wants dead. However, after the deaths of two of them, Timothy himself is killed, throwing the investigation into disarray.

As they lose their only lead, news about the assassinations spreads across Tokyo, leaving the city in a state of panic. It is up to Conan to find and catch the culprit in the hope of putting an end to this sniping spree terror.

[Written by MAL Rewrite]