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It is said that the people of Agartha once coexisted with the Nabateans, the children of the Goddess, but eventually turned away from the Goddess's protection and dedicated themselves to the advancement of technology for their prosperity. In time, they apparently became greedy, arrogant, and imperialistic, eventually challenging the Goddess herself for dominance. The Goddess warred with the Agarthans and destroyed their nation for their hubris. However, the conflict resulted in Fódlan being so devastated that the Goddess was forced to expend all of her energy to heal it, and thus fell into a long slumber in her Holy Tomb at Zanado. The surviving Agarthans retreated underground and their descendants became Those Who Slither in the Dark, who would devote centuries to plotting their revenge.
At some point, Those Who Slither in the Dark secretly manipulated Nemesis into breaching the Holy Tomb and killing the progenitor goddess in order to forge weapons such as the Sword of the Creator and create the Crest of Flames from her body. Nemesis then slaughtered the Nabateans at Zanado and bestowed Crests upon his strongest warriors, the Ten Elites. However, Seiros would survive the massacre, and would go on to gather the remaining Nabateans, the Four Saints, create the Church of Seiros, as well as bestow her Crest of Seiros onto Wilhelm Paul Hresvelg, thereby helping him create the Adrestian Empire. This would eventually lead to Wilhelm following Seiros' will and clashing against Nemesis and his forces, starting the War of Heroes, a war that would span for many decades.
Seiros ultimately prevailed and slew Nemesis in Imperial Year 91, but the failure of Nemesis did not deter the Agarthans from their path. Over a thousand years later, Those Who Slither in the Dark prepared to inflict their vengeance against the unsuspecting people of Fódlan.
A book in the Shadow Library of Abyss titled "Romance of the World's Perdition" reveals that the Agarthans originally worshiped a pantheon of old gods from a land called Thinis.
- In Shambhala, words written in Cyrillic can be seen throughout the city.
- Many of the Agarthans are named after the Seven Sages of Greece; Thales, Solon, Chilon, Bias, Pittacus, and Myson.
- The name Agartha may come from a theory that claims there is a secret land hidden inside the Earth (which it also claims is hollow), known as Agartha.
- While exploring Abyss during the Cindered Shadows side story, the player may encounter a Mysterious Woman who claims to have come to Abyss to worship her gods, as she is unable to anywhere else in Fódlan. Seeing how she specifically refers to multiple deities, it is likely that she is an Agarthan herself, although she lacks their typical pale complexion.