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Shinichi gets involved in a case revolving around an accident from the previous year; however, the case is tied to the black organization who gave Shinichi a drug that shrunk him.
Kaitou Kid announces to the police that he intends to steal the Russian Imperial Easter Egg, which is currently being held in Osaka. As Conan pursues his rival, he discovers that there's more to this case then simply stopping a robbery.
Shinichi is invited to a party held by a famous architect and Shinichi asks Ran to go instead. There a mysterious person plants a lot of bombs and gives Shinichi clues as to the location of the bombs. Shinichi tries to uncover all the bombs and save Ran's life.
As a pair of towers in Tokyo are being prepared for their grand opening, there is a series of murders of people connected to the towers. Conan suspects that the mysterious Syndicate may also be involved.
Mouri Kogoro is called to a special case in the ancient capital of Kyoto. There, Conan meets Heiji and they team up once again to solve the case, recover the stolen Healing Buddha statue, and even discover the identity of Heiji's first love.
A vicious sniper has appeared in Tokyo, rendering the people too scared to go outside, once again it's up to Conan to figure out the meaning behind the killings and capture the mysterious sniper before more lives are lost.
In the story, Kid has his eyes set on the "Lady of the Sky" jewel aboard Bell 3, the largest airship in the world. However, a mysterious terrorist group called Red Shamu-neko has hijacked the airship itself, along with Conan and his allies Kogoro and Ran.
On a dark night, the Japanese police is raided by a spy and different countries' intelligence agencies' secret files are going to be taken, but public safety officers led by Tooru Amuro arrive just in time. The spy steals a car and escapes but is thwarted by FBI agent Shuichi Akai's rifle bullet and falls off the roadway. The next day, Conan and his friends go to an aquarium in Tokyo and find an attractive woman alone and injured. Her left and right eyes are different colors and she suffers from amnesia. Conan and his friends promise to help her regain her memory, so they stay with her. Throughout all this, Vermouth is watching behind the scenes. Afterwards, she pulls out a silencer and speaks into an attached intercom, "It's as planned, Gin."
Kensuke Hanasaki meets a mysterious boy named Yoshio Kobayashi who, due to an unexplained fog, cannot die though he wishes for death. Intrigued by this boy, Kensuke invites him to join the Boys’ Detective Team and their work around the city. But danger awaits and their fate will lead them down a dark path.