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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.

Ran’s secret past revealed! Ten years ago, something happened between her mom and dad. Now, plagued by nightmares, Ran is starting to remember… Meanwhile, a murderous card dealer breaks out of jail to seek revenge. His target: Ran’s father. Can Conan stop him in time and save his girlfriend’s family?

On a dark night, the Japanese police is raided by a spy. Different countries' intelligence agencies - such as England's MI6, Germany's BDN, and America's CIA - as well as the FBI's secret files are going to be taken, but public safety officers lead by Tooru Amuro arrive just in time. The spy steals a car and escapes. The spy and Amuro are then locked in a dead heat on the highway, and just as it is about to cause an accident with multiple cars, the spy's car is hit by FBI agent Shuichi Akai's rifle bullet and falls of the roadway. The next day, Conan and his friends go to a newly-remodeled aquarium in Tokyo. Under the main attraction, a Ferris wheel, Conan finds an attractive woman alone and injured. Her left and right eyes are different colors.

Fifteen years ago in a barren stretch of the Pacific, a cruise ship collided with an iceberg and was lost at sea. More than a decade later, Hideto Yashiro—a ship engineer—died in a fatal car accident. The unlikely connection between these events only comes to light on the luxury liner St. Aphrodite during her maiden voyage. Aboard it on a much needed vacation, Kogorou Mouri, his daughter Ran, Conan Edogawa, and the Detective Boys enjoy a trip provided by Sonoko Suzuki's family. But their fun is soon cut short when a game of hide-and-seek leads to Sonoko's disappearance.

While visiting Hachijo-jima, Conan sneaks aboard a security boat heading to the Pacific Buoy, an off-shore facility constructed near the coasts built to connect surveillance cameras used by police forces around the world. However, an engineer gets abducted! An eerie sound of a propeller hums underwater as a dark figure begins to creep toward Ai Haibara... When the forbidden Black Box is opened, the sealed-away past will surface above the treacherous waves!

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.

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.

Conan Edogawa comes to a bathhouse with Ran Mouri and Ai Haibara. There, he sees suspicious men in the dressing room of the men's bath. However, Conan falls down in the bathhouse and loses consciousness. The two suspicious men, Tatsu and Kondo, take him away in a car. The two belong to the underworld and seem to be working at someone's request. Meanwhile, a woman named Kanae visits the Mouri Detective Agency to request an investigation into her husband's affair. She shows them a picture, and the husband in the picture is one of the culprits who kidnapped Conan.

A new member from the Black Organization that shrunk Shinichi's body manages to find out about Shinichi's transformation into Conan. This discovery starts to put those around him in danger as Gin and the other Black Organization members start to take action.

Police officers around Tokyo are being murdered by an unknown assailant. When Ran witnesses an attempt on the life of one of her friends in the police, she loses her memory. Now, Conan and Inspector Megure must find the murderer while Ran attempts to regain her lost memories.

Once brilliant teenage detective Shinichi Kudo was given a poison that reverted him to a 4-year-old. He's adopted the pseudonym Conan Edogawa so no one (save for an eccentric inventor) will know. Now he's got to solve a series of bombings before his loved ones become victims. Who is this madman and why is he doing this? Only the young genius can save the day but will even he be up to the task?

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.