In the movie, Conan, Ran, and Kogoro are enjoying their trip on the Aphrodite when they begin to notice strange behavior from a man named Goro Domoto. He claims to be a researcher, but his actions make it clear that he is up to something sinister. Meanwhile, a string of mysterious events begin to occur on board, including a fire in the kitchen and a letter that warns of impending doom.
As the voyage continues, the passengers and crew begin to suspect that Domoto may have something to do with the strange occurrences. When a crew member is found dead, it becomes clear that there is a murderer on board. Conan, Ran, and Kogoro work together to solve the mystery, but they soon realize that the killer may be someone they never suspected. As they race against the clock to uncover the truth, the ship becomes stranded in the middle of the ocean, trapped with a murderer and no way to escape.
The story is intertwined with the backstory of the Daiichi Yachiyo Maru, the cargo ship that sunk 15 years ago. It is revealed that the ship was carrying a valuable treasure that is believed to be on board the Aphrodite. The murderer is determined to get their hands on the treasure, and will stop at nothing to obtain it. It is up to Conan and his companions to solve the mystery and save the passengers from a terrible fate.
