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Shinichi and Ran's class decides to take a trip on a boat, but Shinichi decides against going. He quickly changes his mind when he finds a letter of challenge stating that one kid will be kidnapped during the trip. He is eager to accept the challenge, but when the one that vanishes is Sonoko, Shinichi must use all of his reasoning abilities to find Sonoko and protect the other students. When at first he doesn't succeed, he recieves a call from the kidnapper stating he will now abduct another student at exactly twelve noon. Shinichi must now recover from his previous failure and hope to prevent a tragedy. Shinichi receives a letter from an unknown challenging him to stop a kidnapping from happening.