Plot
Fifteen years ago, a cargo ship named Yashiromaru, built by the Yashiro group, sank while colliding with iceberg. Fifteen years later on a new on a 100 million yen luxurious cruise ship named the MS Aphrodite, also built by the Yashiro group, Conan Edogawa and the rest were invited to the cruise through Sonoko Suzuki. Earlier, the husband of the CEO of the Yashiro family group, an established ship architect, apparently had a heart-attack and drove his car down a cliff.
On Aphrodite, the CEO herself was found murdered in her room. Later, her father, the president of the Yashiro group was also found missing. He had been thrown off the cruise into the ocean, seemingly by the same person. At the welcoming party, Kogoro Mouri shows off his deduction skills, and concluded that the sub-designer of the cruise, Minako Akiyoshi, was the murderer.
However, Conan has different ideas. Hironari Kusaka, a scriptwriter who worked in co-operation with Akiyoshi on a script, was the culprit. Kusaka reveals to Aphrodite captain Wataru Kaido that the accident from 15 years ago was a scheme to sink Yashiromaru deliberately to get insurance. His father was murdered when he discovered the captain of the ship was drugged by Kaido when he was a vice captain and left to die. Kusaka immediately set off bombs and escaped by sea and the Detective Boys gave chase.
After they, Juzo Megure, Ninzaburou Shiratori and Wataru Takagi of Tokyo Metropolitan Police Department successfully took down Kusaka, more bombs were ignited. All passengers were evacuated, but Ran returned to her hiding place during the hide-and-seek game to find a "gold medal" made by sea-shells the Detective Boys made for her. However, as Aphrodite swayed, she fainted in the enclosed area. Just before Kaido evacuates, Akiyoshi takes him hostage, turning out she was the real murderer after all, and was the one who did all three killings and made Kusaka think that he did them himself.
Akiyoshi also revealed that her father was the captain who died while Yashiromaru sank. Kogoro, however, deduced correctly this time and managed to subdue Akiyoshi. He was originally trying to find evidence to prove her innocence because of her strong resemblance to his wife Eri Kisaki, but the more investigation he does, the more guilty she became. As Kogoro and Conan began to evacuate, they found out that Ran was missing. They find her under the deck of the boat with the help of a fire axe. Afterwards, a helicopter of Japan Coast Guard comes and picks them up, just before Aphrodite sinks stern-first to the bottom of the ocean.
In the post-credits scene, Conan explained he knew where Ran was because when he kicked the volleyball, Ran said she heard a soccer ball, meaning she was in a place with a tough wall. The Detective Boys come, and told Ran they made a better "gold medal" for her, and put it on her.
