Despite being pretty disappointed by Nier, I'd still like to get some closure on elements of the story that were not clear to me. I've read a few discussions on these topics and haven't really come across satisfying answers to them, perhaps I'll get them here.

1. Who created Yorha originally? In some ways it seems suggested that the machine consciousness/red girl/whatever created Yorha, but this doesn't make sense.

2. Somewhat in relation to the above the above, the machine consciousness is supposed to have engineered this repeating cycle where Yorha gets mostly destroyed, but then is allowed rebuild to serve the machine consciousness's evolutionary goals. But who is rebuilding Yorha and creating the next series of androids? The few androids left alive at the end of the "purge" don't seem like they're in any position to re-establish a space base and create an entire new series of androids.

3. Why the hell does 9S exist? Yorha builds an android destined to figure out the lie of Yorha, then builds another to destroy 9S and keep that lie safe. Why would they even make an android like 9S in the first place then?

4. I don't understand the origin of the androids in general. Humans were already dead when the aliens invaded, yes? So the androids must not have originally been built for the purpose of fighting the aliens. Why were they built? What were they doing in the intervening years between humans dying and the aliens invading?

5. The aliens motive for invading was?

That's it for now I guess. May have more as I try to piece this mess together.

1. Yoko Taro has done a lot of interviews, and in one for the guide or something he specifically deflects a question about the Yorha creator. She's another android. Anything else is a mystery, besides certain things she established(the yorha units wearing black, presumably because of the black boxes inside of them, for one thing).

2. There are several more orbital bases, housing regular androids. I suppose they were unharmed when the Yorha bunker blew up. This was also in the interview above. Even if the Yorha died out for good, the regular androids have been fighting for centuries, and could continue to do so.

3. Scanner units are a necessary part of the Yorha, for their hacking capabilities. The reason they don't put in a program that forbids them from finding out the truth, or just teach them to deal with it or whatever, I couldn't say, except that it's a more tragic story that way.

4. The androids were built to oversee the Gesthalt project in the original Nier, since they're basically immortal and unaffected by the disease that took humanity. I'm not sure how they ended up where they are today, I can only assume it's either described more in detail in the original Nier, or I missed a detail. Though I remember the Popola & Devola text adventure mentioning there were other copies of them in different towns.

5. There is no known motive. The aliens are dismissed even by their own creations as dull and uncreative, and nobody knows much about them. Judging by the secret final boss and some of the cutscene artwork for Emil's memories, they only developed their robots by mimicking Emil in the first place.

I feel ya, I think I made a thread like this when I was done with the game too. I feel like too many details are only told in supplementary materials like interviews. But also, it's not really a game with a lot of strong explanations for what happens. It's there primarily to create an emotion and support the themes. It's not coherent sci-fi in the way Mass Effect 1 or Horizon Zero Dawn is. Why do robots become wild cannibals even though they're off the machine network? Why does the giant sea monster attack? How come all the robots in the park become zombie-like? Why does the robot messiah die and the death cult start murdering one another? Is that Yorha chick in the desert oasis aware she's the only one left? How can Adam and Eve control half the machine network each, but actually there's a whole another AI behind them?

@redhotchilimist: I never came across that Q&A, thanks for that and the responses in general.

I felt being tied to the whole lineage and crazy backstory of Drakengard and the original Nier did the game a disservice, and it would have been better with a fully self-contained backstory, but I guess creating crazy narrative lineages is common for Japanese game auteurs.