I had a feeling the opening had something to do with the ending. I had wondered how she would end up like that, and well, defying your mother from joining forces and taking over the above ground is 100% qualification for petrification.
As for the backstory, I am torn between whether or not Naija was actually raised by Mia. If you think about it, The Creator loved Mia a lot, so she probably was to stay with him down in " The Body" or wherever his spirit actually lay (since he also had a spirit in the Sunken city, correct? Or was that another ghost boy?) If you think about the different age stages of Naija in her memories (baby in Abyss, young in Mithalas, preteen(?) in the Veil) shows that Mia probably left The Creator shortly before or after she created Naija, hence the cradle in The Abyss. So that might have been Mia after all, but she either must have become crooked in her powers and changed over time, or, Naija was planted in Mithilian society (it's obvious she lived there.)
The boy on the airship is most definitely her son. I swore I heard someone say "Mom or mother" after he took his hand off the crystal but that could be me just making stuff up and hearing things. Whatever the case, he looks a great deal like Li, except with green skin and apparently amphibious lungs so he's most certainly their "hybrid" son. The sleeping girl, at first I obviously thought that could be his sister, since she too had dark hair like Li, but her clothes looked Mithalian. then I remembered there was mention of a Mithalian princess, so I thought that might be some sort of lost member of the royal family that escaped the slaughter that had occurred and she has been alone all this time, somewhat like Najia. Just a thought, a far fetched one at the very least but it's still a theory. I might have to beat the game again to see that, where she was sleeping exactly.
What is considered the "good" ending, did I see that? I'm pretty sure I got all the memories since she didn't tell me to look harder aka you rushed. I thought I saw a wedding screenshot somewhere, but there was nothing of that sort in the ending, was that a mod?
I immediately saw the eagles on Li's camp as pertaining to a city or government. I think he was there again under orders to look for something, or was just studying. If I can remember correctly, did he have glasses when he was a child? I thought of him more as a scientist than a person from a government, not many people from government go scuba diving. Seemed he was doing research.
I'm a bit confused about the little ghost boy, was that Eric? Or a representation of him?