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 receives 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.
The culprit is Mai Nishida. She was the girlfriend of a man who Shinchi got arrested and that man died in prison. He ran a wholesale company but helped in a crime when he was cornered in debts. She tied a rope on the boat and a sack and put a combustion device to burn the rope to make it look like Sonoko jumped to the water. Then she kidnapped Sonoko for real at the closet inside the box, which she used a mirror to make it look empty. The second kidnapping isn't really a kidnapping, but Ran do this on her own. Nishida sneaked a threat and a spare key to her room. When the lights go out, she immediately open the lock, coming out, lock the door, and disguised as a police guard to go to the abandoned house. The suicide is a murder and the culprit forced Azuma to write a will to make it look like a suicide and kills him. The proof that Mai was the kidnapper is the will. When shining the will on light, it will say Kidnapper A->Ma i.