Storywise, its like someone bringing you to the edge of a deep, dark pit. Its scary, but you still want to know what's at the bottom. Some people might even feel compelled to fall in.
I think that's how Naija would have felt. She knew there was some negative presence out there, and she wanted to go confront it and resolve it, even though she didn't know exactly what it was at that time. There was also the inevitable pull of chaos, entropy. (like the idea of gravity and the pit)
I think while it was frightening to Naija initially, it helped prepare her for what she felt she had to do to rescue Li at the end of the game: kill the Creator. This is ultimately what Mia wanted her to do.
There's also the element that while Naija is afraid of killing, she also loves doing it to a degree. (a degree partially determined by the player) Naija is both drawn to and tries to stay away from that kind of power.
Some of the dialog tracks how she's feeling about it, e.g. after killing the rotcores in Mithalas... she wonders if what she's doing is right.
By the time Li is captured, she's comfortable enough with killing to become filled with defiant rage, and feels its her right to take revenge. I think that's the only story point where she decides to pursue one of the bosses and destroy them, rather than being trapped by them.
There was originally going to be dialog from Naija's son in the optional ending to the game, talking more about Mia's effect on Naija. (the idea being that he was really the main character all along, and Naija's adventures were part of a larger story)
(this comes after the mia + naija confrontation/talk)
Secret Ending Part 2
Naija’s Son:
That’s how I found out where mother was. The crystal in our home had told me everything.
I know now that Mia captured her. I can’t bear to think what that witch wants to do to her…
Time is running out, and I have to leave.
I suspect I’ll have to fight… and kill. Father warned me about that. He also saw into mother’s mind – saw how she was changed. How she became a weapon…
I’m determined to save her, no matter the cost.
I’ll try to leave you many memories as I travel. Remember that you’ll always be in my heart, no matter what happens.
I miss you already, but I’ll be back before you know it.
...farewell…
Secret Ending Part 3
Naija’s Son:
The Verse flows throughout Aquaria. Through each ripple and wave. Through every living being.
The Verse binds us all as one.
The Verse binds us, narrator and explorer. My story will become your own, and yours will become mine. You will live my life through my eyes…
and you will learn the truth.