- Adam & Eve. They are the first two manifestations of the machine's attempt to essentially "hijack" humanity. In C/D they're dormant ... you kinda killed them, but the main networked machine (Girl(s) in Red) keeps their code & memory, which is how they're all goin' to the moon together.
- Collapsing tower ... I think it's designed to collapse with the launch, and the launch happens in C/D/E no matter what. Just think about the towers and whatnot that come down when we launch rockets into space these days. I think the machines knew it'd be like that when they were building the place, which may have been going on for thousands of years. Also provides for a nice climactic ending: crumbling buildings are the stuff of endgame scenarios. :)
- Adam states quite clearly that the machines killed all the aliens. He didn't say how, or how long it took, or if machines are on a home planet far away and those machines ALSO killed aliens, or what year(s) the genocide happened. But if we are to believe Adam, they're all quite dead. It's important to remember what we know about these so-called aliens: apparently, they had a plant-like cell and organ structure ... so, too, do the machine cores, and so, too, do the Android black boxes. I don't think Androids always had black boxes (Devola/Popola pairs didn't have them...? If they did, I think that's what Dev/Pop would've *used* on NieR and crew in the first game!). The YoRHa androids get them once the YoRHa program begins, but they are definitely reverse-engineered based on machine cores, which were reverse engineered based on the structure of these apparent aliens. The existence of these aliens remains one of the big shoulder-shrugs. There's no supplemental material that talks about them ... yet. I have my own theories.
- The voice speaking to them is the networked machine, which is personified as the Red Girl(s). The Red Girl(s) are the visual representation going as far back as the YoRHa Stage Play. I think if you study them, though this is my opinion, it looks like Yonah wearing a red dress. I could be off base. In any case, play through the game again and you'll see that the Red Girl(s) are always watching. They appear in the 9S ending (B), watching you there. In a scene before the YoRHa satellite is destroyed, when you descend on a flight unit to earth as 9S, you can see one of the red girls watching you.
- Who *started* YoRHa? That's a really good question. I don't think the stage play gets into it. What we can say for sure is that it wasn't created by anyone who serves in it, unless they had a full memory erase before entering it. My best guess? A handful of androids that weren't in YoRHa but who had a crazy plan to re-motivate their kind decided to invent YoRHa as a sort of noble lie ... I think this is Yoko Taro's version of "tell society there is a God so they will behave" -- in this case, behaving means surviving and fighting against machines, not passively letting them kill you all. Taro stated definitely that no matter what ending was "canon" in NieR, all humanity would be dead (it's D by the way, where all memories of NieR are wiped, though Emil seems to remember, envision him juuuust during the end of the super-optional fight, which you probably still need to do...). Emil *was* human, but the Hamelin group made him human+Maso (the crazy energy black-dust shit that came from Drakengard), hence creepy-head. This lets him live on, and he sees humanity die out. There is a Japanese graphic novel that covers this, and even goes into a scenario where Emil and Kainé fight some asshole who is manufacturing "evil androids" -- Kainé dies in that battle. Anyway, YoRHa's design and existence comes about because 85 million Emil-duplicates can't hold off the aliens forever and *someone* has to come up with an alternative. It IS possible that Emil, or Emil with some android co-conspirators, design YoRHa in an attempt to give Emil some reprieve so all his clones don't go batshit crazy and destroy everyone. His self-preservation needs (including memory) had to kick in at some point, and it's only after YoRHa really starts fighting back that Emil can catch a break. So that would be *motive* for Emil to design it. And then forget he designed it, because his memory is shit. So... literally no one would know it was all a lie. Except A2.
An additional question to consider: what happens when red girls / Adam+Eve / possibly 9S (in code form) reach the Moon? Consider the hexadecimal code I pulled from the liner notes of the soundtrack. Remember, the MACHINES think they're gonna find a bunch of humans. 9S knows that all they're going to find, at best, is a tiny repository with partial human DNA and maybe some databanks on human history and culture that couldn't be found elsewhere. UNLESS there's a double-lie and a real human made it ... but again, Yoko Taro doesn't lie, that wouldn't happen. DOUBLE-BUT! "The End of YoRHa" is complicated, because the game states at some point that a handful of YoRHa soldiers are actually stationed on the moon to protect it ... they apparently don't know the truth that it's the only thing there, but they think they're supposed to guard that area for the sake of humanity. Those androids could become key players in some future story.
ONE LAST THING -- with 1mil sales, SE might regret the apparent fight they had with Yoko Taro about expansions / DLC. If they regret it enough, we might be lucky enough to get a stand-alone A2 scenario telling the story of the Pearl Harbor mission. Which would be so epic.
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