After participating in the opening ceremony, Conan, Professor Agasa, Ran, Haibara, and the Detective Boys are enjoying the view from the observation deck of the 635-metre tall Bell Tree Tower. Suddenly, a bullet breaks through a window, strikes a man's chest and breaks a TV screen, causing everyone to panic. Conan stays calm and, using the zoom function on his tracking glasses to follow the path of the bullet to its source, spots the sniper. He and Masumi Sera, who had been present at the Tower as part of an assignment to shadow the victim, pursue the fleeing culprit on Masumi's motorcycle, but the chase takes a violent turn when the suspect uses a handgun and even hand grenades to take out his pursuers. Even the FBI get involved in the chase, but the culprit and the mysteries of the sniping end up vanishing into the ocean.

The investigation turns up a connection to the special United States Navy squadron, the Navy SEALS and other former US military officers working in Japan. However, the first sniping was just the beginning; as more people are shot, the citizens of Tokyo panic! What is the meaning of the rifle case and dice left behind? As his investigation progresses, Conan soon finds himself in the sniper's cross-hairs, only to be saved by Masumi who intervenes and takes the bullet in his stead. And, in the background, Subaru Okiya begins to make his move...

The sniper/culprit is Kevin Yoshino, while the entire murder plan was created by his master Timothy Hunter. Kevin became Hunter's student and helped him carry out the plan because he wanted to repay Hunter for saving his life during their war operations in the Middle East.

The reason for the serial killings was that Waltz was jealous of Hunter's achievements, which belittled his own actions. Waltz set Hunter up so he wouldn't get the Silver Star. He even ordered Murphy to assassinate Hunter, but the bullet failed to kill him, although a fragment of it remained in Hunter's skull and damaged his optical nerves, severely impairing him. Yoshino eventually discovered the deception, but Waltz destroyed the evidence before it could be used in court, driving Hunter into conceiving his revenge plan. The five sniping positions used for the murders, if viewed from ground level, combine to form a pentagon, which marks the five points of a Silver Star.

Kevin attempted to kill Waltz, but Conan saved the latter by kicking a ball at him to knock him out of the bullet's way. Kevin then attempted to kill Conan, but Subaru saved him. Ran, unaware of Conan's plan of saving Ayumi decides to go after Kevin herself but trips ends up being Kevin's target. She is saved thanks to the combined effort of Conan and Subaru, and she manages to take Kevin down after that - for Ayumi, for Sonoko and for Sera. In the end, Subaru Okiya answers a call from James Black with Shuichi Akai's voice.