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Kaitou Kid sends a riddle, warning of another heist. The police deduce that his next target is a recently discovered Fabergé egg belonging to Nicholas II of Russia, which is to be displayed in the Suzuki Modern Art Museum in Osaka on August 22. The night of the heist, Kid successfully steals the egg and flies off with it, and Conan tenaciously chases after him with Heiji. However, in the middle of the chase, Kid is shot in the right eye by an unknown assailant and apparently falls into the sea to his death. After recovering the egg, the police fruitlessly search for Kid’s body.
The next day, Conan, Ran, and Kogoro board a boat to Tokyo. They meet Natsumi Kousaka, whose great-grandfather worked in Fabergé’s factory. She shows them a part of a sketch of two eggs and a key, which were found among her late grandmother’s momentos. Conan suspects that the person who shot Kaitou Kid is on the ship. That night, Ryu Sagawa, a freelance photographer covering the press with news of the egg, is murdered, shot in the right eye in the same fashion as Kid. Soon after his body is discovered, Inspector Megure, along with officers Takagi and Shiratori, arrive by helicopter to inspect the crime scene. At first, they suspected Sonoko’s father’s servant, Mr. Nishino, but the police and Conan later conclude that the culprit is Scorpion – a mysterious killer who always shoots his victims in the right eye. A missing lifeboat hints that Scorpion has already escaped, and the passengers of the boat set off toward Yokosuka Castle, the location of Scorpion’s next target: the second egg.
While exploring the castle, the group stumbles across secret passages beneath the castle. As they traverse the tunnel, Inui, an art dealer, sees a shadowy figure in one direction of the tunnels, and in his pursuit, he is shot by a silenced handgun. Delving farther into the tunnel, they find a coffin with a corpse clutching the second egg. Suddenly, the two eggs are snatched away.
Conan deduces that Scorpion is Seiran the historian. She shoots her victims in the right eye to avenge her ancestor, Rasputin, whose body was found with an eye missing. Seiran attempts to kill Conan with her last bullet, but the bullet ricochets off the bulletproof glass on Conan’s glasses installed by the professor. As Conan kicks a piece of rubble, she reloads and is about to fire when a playing card knocks the gun out of her hands. Conan then knocks her out with the rubble. Shiratori appears and carries Seiran out. Conan figures “Shiratori” was actually Kid in disguise. In the end, Conan is about to confess to Ran that he’s Shinichi, but then Kid comes, disguised as Shinichi, and distracts Ran. The Phantom Thief then disappears in a flurry of pigeons.