A terrorist group invades a laboratory containing a deadly bacteria and destroys the lab with an explosion. They later announce via the internet they have gained possession of the bacteria and declare themselves to be the Red Siamese Cats, a terrorist group that was eradicated a decade ago.
Serial murders involving all kinds have happened. All the victims are from a Music School led by a famous pianist. Conan and company have been invited to a opening concert of the Music Hall built by the pianist. The biggest attraction of this concert is the world famous violin called "Stradivarius" and a special appearance of a singer who has perfect pitch.
Kaitou Kid dares to challenge the police once more, setting his sights on the Russian Imperial Easter Egg. With the date, time, and place, the Osaka police force scrambles to stop him. But this time, Kid may have bitten off more than he can chew—Conan Edogawa, Heiji Hattori, and numerous others are also trying to get their hands on the jeweled egg.
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.
Shibuya, Tokyo, is bustling with the Halloween season. A wedding is being held at Shibuya Hikarie, where Detective Miwako Sato of the Metropolitan Police Department is dressed in a wedding dress. While Conan and the other invited guests are watching, an assailant suddenly bursts in, and Detective Wataru Takagi, who was trying to protect Sato, is injured. Takagi survived and the situation was settled, but in Sato's eyes, the image of the grim reaper that she had seen when Detective Matsuda, the man she had been in love with, had been killed in a series of bombings three years ago, overlapped with Takagi's.
Set in the year 2000, when the level of Labor accidents begin to escalate around Tokyo Bay, police detectives Kusumi and Hata are assigned to investigate. What they discover leads to a series of government cover-ups, conspiracy concerning a new biological weapon entitled WXIII-Wasted Thirteen and a tragic, personal connection to Hata. The only hope to stop this threat is to cooperate with the military and lead WXIII into a showdown with the Labors of Special Vehicle Division 2.