I had the pleasure of visiting Gunkanjima a few years ago. If you're in Nagasaki, there are a few tour operators that ferry you to the island for a tour. Unfortunately you can't explore on your own for safety reasons, but still an amazing place to visit.
About the first one, the story goes like someone stopped the wave of flood holding the holy book in hand. Flood had already taken those buildings partially but it stopped and went back. That's how the story goes about this. I might be misremembering some parts though.
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