How I'm interpreting all this (heavy spoilers ahead) :
On the archbishop's final moments light is fading away from him. So it's not that there's something dark about us, that's just a representation of his life extinguishing, we just happen to be on his field of view at that moment. I was confused by this at first, because of the mix of that darkness, what he asked -"Who- What are you?!"- and our character's expression afterwards, which at quick glance may look like an evil grin, but I think it to be a worried expression instead.
So, he's questioning both our nature and our purpose. Until now we think we're an entity sent by a higher being -the planet itself- and never questioned it. But what if we're something else? We've always cared only about our mission and never about ourselves, and the people around us have never wondered nor questioned our nature beyond being the "warrior of Light". Nobody researches what a "warrior of light" is. I think the archbishop is the very first character in the entire game to make the honest question, so only now we're left wondering the same. What kind of freak are we?
And a freak I think we are. By what we've learned on Heavensward about summoning I think it's entirely possible that we're nothing more than a primal, channeling the people's hopes for a champion to save them and sustained by Hydaelin's aether. And I think the warrior of darkness is another such primal.
By the way, I also think it's possible for that Nanamo that woke up to be another primal channeling the people of Ul'dah's faith on her leadership and that the real Nanamo is actually dead. (It would give Lolorito's nonsensical schemes some meaning at least)