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.