Nobody knows why. Some blame the gods, or certain subsets of gods. Some blame the nobility, which threw off the shackles of the Aedyr Empire not that long ago. Still others blame animancers — scientists studying the nature of the soul. After all, animancy seems like a good enough place to start when casting blame around for soulless babies.
And then there's you. You have the opposite issue — your soul has "Awakened." Each soul in Pillars of Eternity is subject to strict rules of reincarnation, so when a person dies his or her soul finds itself in another body, though without any memory of its past selves...except when Awakened, like you. You remember flashes of your past lives, and can actually see other people's past selves as well.
Why you? That's the initial question that sets you wending through Dyrwood, trying to uncover your own fate while also surviving one of the most tumultuous game worlds I've ever experienced. Dyrwood is basically a revolution in the making. The peasants hate the nobility. The nobility cloisters itself away from the peasants. The Galfathans — a tribal group living in the wilderness — hates the people of Dyrwood. Everyone hates the animancers. And there's this whole Hollowborn epidemic hovering over it all.
I don't want to spoil much more, but the story so far is fantastic. Sure, much of it can reduce down to the age-old "random person saves the world" trope, but it's really the amount of care put into presenting the world that sets Pillars of Eternity apart. It's the way you'll read a random book and then six hours later realize that book was actually intrinsic to a conversation you're having, not necessarily in terms of actual conversation options but just because you have a deeper sense of the world itself.
It's also interesting how the lore mirrors questions from our own world. You can clearly see shades of debates about stem cells or the role of religion in government or "Has science gone too far?" in Obsidian's world, albeit couched safely in fantasy. And who's right? Well, nobody really. Animancers aren't necessarily evil, nor are the people against animancy. It's all shades of gray here.
Side note: Turn off the metagame information in conversations. You can have the game tell you whether specific responses are "Benevolent," "Rational," et cetera. Disable those indicators and just play. It's way more interesting to see how your character's dialogue is perceived when you don't know ahead of time.
The story is bolstered by fascinating party members: The priest who looks so insane he scares people walking down the road, for instance, and the hulking Aumaua (a race) who, despite his size and strength, is mostly at your side so he can continue his scholarly pursuits. Or the ranger who spent the last five years scouring the earth in search of her former tribe leader's reincarnated soul.
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