Noah's Ark—the latest in VR technology and a milestone of human innovation—is set for a showcase to Japan's privileged children. They have the honour of beginning a new revolution in gaming; however, their carefree fun is cut short when a company employee is found murdered, with his dying message pointing to a clue hidden within the Ark. Along with the Detective Boys and Ran Mouri, Conan Edogawa enters Noah's Ark to solve this mystery and ensure the perpetrator is caught. But once they're inside the Ark, it takes on a mind of its own, imprisoning them and the children within its worlds. To escape and bring the murderer to justice, Conan and company must navigate a simulated 19th century London and track down the infamous Jack the Ripper—with the lives of 50 innocent children depending on them.

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. Some time later, the CEO of the Yashiro group, who built the St. Aphrodite, is found stabbed to death and her father missing. While the police's investigation turns to a dead end, Conan closes in on the culprit. Unwilling to be apprehended, the culprit threatens to blow up the St. Aphrodite and sink all her passengers. As the ship's hull rapidly fills with water, the truth behind the vengeful murders is finally revealed. With no place to escape, Conan and Kogorou must wrestle with the elusive culprit before everyone on board is dragged to the ocean floor.

Under the cover of darkness, a masked samurai murders five men across the metropolis of Japan: three in Tokyo, one in Osaka, and the last in Kyoto. In their investigation, the police learn that each man was a member of the Genjibotaru—a thieves gang centered on the theft of Buddhist statues and artifacts and who go by the names of Minomoto no Yoshitune's servants. Without a clear motive or clues to the other members' identities, the case runs dry until a Kyoto temple calls for the famous Kogorou Mouri. Having received an anonymous letter containing a peculiar puzzle, the temple monks ask for his assistance in solving it to recover their long lost statue. Meanwhile, Conan Edogawa and high school detective Heiji Hattori team up in order to solve the cryptic puzzle and find the murderer, as Hattori searches for his childhood love. With Hattori's knowledge of Kyoto, the two scour the streets and gradually discover the truth, but not before the murderer strikes again—killing another Genjibotaru member and, after repeated attempts on Hattori's life, eventually kidnapping Hattori's childhood sweetheart. It is only by working together to bring buried clues to light can Conan and Hattori hope to end the rogue samurai's bloodshed and save Hattori's love.

On a rainy afternoon, the Detective Boys witness a murder across the street. Barred by traffic, the culprit slips away and Conan Edogawa is left a single clue by a dying detective. Days later, another detective is found murdered in a parking lot, leaving the police rattled. Suspicious that the culprit is one of their own, everyone in the police department without an alibi is suspect. But despite being on high alert, they are outmaneuvered and suffer yet another attack—this time with Ran Mouri finding herself in the crossfire. Traumatized, Ran wakes in the hospital with retrograde amnesia, remembering nothing about her life. Soon released, she struggles to remember her past and grows fearful of not regaining her memories before being targeted by the killer for what she witnessed. As she is guarded by friends and family, it is up to Conan to piece together the clues and find who the murderer is before they strike again.