Fifteen years earlier, a desolate Pacific stretch saw a cruise liner strike an iceberg and vanish into the deep. Over ten years later, shipwright Hideto Yashiro perished in a tragic automobile crash. The strange link between these incidents surfaces only aboard the opulent St. Aphrodite on its inaugural run.
On a much‑needed holiday, Kogorou Mouri, his daughter Ran, Conan Edogawa, and the Detective Boys enjoy a journey sponsored by Sonoko Suzuki"s relatives. Their merriment is abruptly halted when a game of hide‑and‑seek causes Sonoko to vanish. Later, the Yashiro Group"s chief executive—who commissioned the St. Aphrodite—is discovered stabbed, and her father is missing. As police hit a dead end, Conan narrows in on the perpetrator. Determined to evade capture, the assailant threatens to detonate the St. Aphrodite and doom all aboard.
With the vessel"s hull flooding swiftly, the motive behind the vengeful killings finally comes to light. Stranded with no escape route, Conan and Kogorou confront the elusive villain before everyone on board is pulled to the sea floor.