I finally completed this game today (Ending C/D/E) and can finally enter the spoiler topic! I do have a few questions, though. My apologies if these have already been answered, but this thread is rather large to sort through.
1) From what I understand, Androids already existed before the Alien/Machine life-forms hit (never played the original Nier, but considering Devola/Popola are Androids and existed during that time-frame, it's clear they were around). Where were they made? I originally thought it was the Bunker that created/sent them out, but considering the whole idea behind that was only to serve as a temporary rally effort to continue the war against the machines (and not as a permanent form of residence), as well as Androids existing long before the Bunker was even a thing, makes me question where all of the Androids were assembled.
2) 9S mentions that the YoRHa squadron were created to be destroyed, hence the backdoor plan and the installation of the Logic Virus. I get why there had to be YoRHa members, such as 2B/2E, to "silence" -S models who got too close to the truth, but why was it decided to ultimately end them? Why forcibly cause a reset when/if the Android side were so close to winning? Also, on the subject of the Logic Virus, did they explain how it was formed? I just assumed it was due to the mismatch of Android/Machine parts, that ultimately caused YoRHa members to become corrupt, but from the sounds of things it was planned (as a means to kill of YoRHa). But then, judging from the Pearl Harbour records, Resistance members that weren't part of YoRHa were also affected, so I guess that kind of disproves that theory.
3) What exactly was the Ark? Was it just a means to gather information/data on the current planet (as well as resources), to later shoot off into space to colonize another planet after leaving the current one? Or was its primary goal simply to destroy the Moon, the last place where human data was stored? At the end of Route D, it sounds like all of the "souls/cores" of the defeated Machines within (i.e., Adam/Eve) were being sent to some other planet (which may or may not make the journey, according to the Terminal). Was the Ark Alien or the Machine-made? The reason I ask is because it resembled a lot of the Copied City, which Adam created.
I think that's everything. I still need to let everything that happened marinate in my brain for a bit. There's a lot to process. :/