So, if you go into the files that make up the game, in the gfx section you can find a set of files for "lucien-baby", "lucien", and "luciengf". If you look at the file names for the soundtrack, and look at the graphics, clearly Lucien is the name of the son of Li and Naija. He presumably was raised mostly by Li. He extracted Naija's memories from the soul crystal you see him standing at, immediately after the Mia/Naija scene. Apparently when he grew up, he got a girlfriend -- maybe a Mithalan? -- and you see her sleeping alone in Naija's old home. I think Lucien may've left her behind without informing her he was taking off to track down Mia and Naija.
Relatedly: Holy shazbat is Mia bad news. She's even worse than the Creator (or really, the spirit that bonded with the boy to form the Creator -- it sounds like the boy, by himself, was a sweet kid). Creator just wanted to dominate his own creations; Mia wants to conquer the world, and is willing to subvert the conscious will of her own daughter to do so. Megalomaniac, much?
If you're interested -- I'm on a Mac, and the way you get at these files is to right-click or ctrl-click on Aquaria.app, and then select the "Show Package Contents" menu item. (You can do this on any app, actually.) Then you can dig around to find various interesting graphics, sound, and scripting files. (If you're really clever, you can even find ways to have arbitrary enemies drop arbitrary food, find the file that defines all the recipes, and so on.
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