I figured that the person who lived where the well stood was actually Bongo-Bongo in life, capturing and torturing people there while using the Lens of Truth to see through his traps. Eventually, in the Fierce War or by the Sheikah's hands, possibly even old age, he died. Impa demolished his home and sealed his soul where it once was. He may have been inspired by the Shadow Temple, or he could have been building his labyrinth to eventually connect to the Shadow Temple.

Also, the skeletal face seen everywhere might be the face of some dark deity.

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