I have a dozen or so 'truth bombs' hidden in my campaign setting that rock the PCs preconceived notions of their universe when they are revealed. When I assembled my world in the 1980s, I was reading a lot of sci-fi that addressed the truth behind the facade, and that highly influences how the world came together. I layered the depth of a deep story beneath the superficial simplicity of a short story. A lot of those stories have evolved - a lot - since then, but the basic premise I took then applies still today.
1.) Figure out who the powerful beings are.
2.) Look at what common lore is about them. Assume that is the general view of these beings.
3.) Ask what real world inspirations might be behind those images. Then, ask how those people would see themselves.
4.) Figure out how to reconcile those two views.
This generally gives you the story everyone knows, and a deeper story that is less black and white. That results in a lot of interesting storytelling as heroes rush off to destroy the bad guys only to start questioning whether there are any good guys in the story at all (there always are, but they are decidedly rare - just like the real world).