A man is shot to death by his subordinates, they call themselves the Organizer of Shadows. Twenty years later, Conan helps Ran and Mouri solve a puzzle which wins them an all-expense-paid trip on a giant boat built for a small number of people. After 11 people have entered the boat, the boat leaves. Mouri meets an inspector he used to work with on the boat and meet up with Heiji Hattori. After a man is murdered, they learn a man named Kanoi who was the leader of the Organizer of Shadows is on the boat. After a bombing, and discovering two dead bodies, Conan solves the case, realizing there were two separate culprits; one as the bomber, and one as the murderer. They were part of the Organizer of Shadows.