In Final Fantasy XVI, Ultima gives us a brief history of the world. His race's world was destroyed by the Blight, so the survivors fled to Valisthea to harvest its aether (the purpose of the Mothercrystals) and craft a vessel to hold the power necessary to create their new world, free from the Blight (the purpose of humanity and ultimately, Clive). I would guess that the Fallen are the original humans before they became self-aware and woke to self-determination.
We destroy the last Mothercrystal, only for Ultima to create a new one, the "very obvious final dungeon" Origin. Ultima talks about the Logos, which is the ancient Greek word for, well, "word," "thought," or "reason." Wonder what the significance of that is.