After receiving a distressing correspondence from a former classmate requesting his presence, high school detective Hajime Kindaichi travels to Twilight Island to investigate the anguish behind the letter.

Meanwhile, as fate would have it, Conan Edogawa has been introduced to a modern folktale by Professor Agasa, on an island in the south that serves as a premiere tourist resort, inhabitants have been mysteriously disappearing for extended periods of time before suddenly returning without explanation. What's more: When they disappear, they are transported to an alternate version of that very same island. Intrigued, Conan consents to investigate the case while his companions go on a vacation at the tourist trap known as Twilight Island.

As the mystery deepens and it becomes clear their two cases are more related than it first seemed, a grand case unfolds that requires the unmatched reasoning powers of both young detectives.