If the Bunker was destroyed, why would the infected Operators be on the "Ark"? Operators don't go in the field, and there was no signs any of them escaped since the Commander self destruct the Bunker.
There weren't any operators? If you're talking about 21O the battle confirmed that she redesignated herself as a combat unit when YorHa was going in for the kill after adam and Eve
I don't understand the Ark. It was created..when and by who? The machines?
It was hiding under ground this whole time, or built by Adam?
Was the "Copied City" area part of the Ark?
It was aimed at the moon, but when the machines realized that it was all a lie, they decided to turn it into an Ark?
The tower was initially created as a giant ground-to-space cannon aimed at the human server on the moon, but as shown in ending d, the machine consciousness, having discovered the futility of the never ending war through their evolutions, decided repurpose the cannon and created an ark to allow the machine lifeforms to have a new life in a different world.
The copied city is a different thing but i think it's meant to show that the machines are able to create complex structures using that white material.
It had the capability of creating Androids? Why were there so many models of 2B?
I think either they took the copies to yorha already had (remember that everytime you died you're supposedly getting a new body), or yes, they are capable of creating Android like machines as shown by adam and Eve. And also in the end, they are all the same really.
A backdoor was installed on the YorHa servers on purpose, because they knew that the machines will hack it? Why did they choose THAT specific time to open the backdoor? Was it because Adam and Eve was destroyed and they thought it was a great time to "open" the backdoor? Going by when Adam and Eve was revealed, they couldn't have anticipated Adam and Eve existing or their destruction. And it looks like it was hacked specifically by the AI twins, were they the only ones capable of hacking the Bunker? If so, did the original creators of Project YorHa anticipate the evolution of machines and knew that "one day" a machine could hack the Bunker?
The backdoor was created to open precisely when yorha has the overwhelming advantage over the machines. Could be when adam and Eve happened, and it could have also opened it when yorha was confident enough to go all out war mode when most of the time they've just been doing skirmishes. I assume that the machines knew about it for a long time and was just waiting patiently for it to open. The ai twins are just the manifestations of the machine consciousness.
The "infection"..was it created by YorHa? Where did it come from? Is the purpose of it designed from the beginning since YorHa was designed to end? If not, what was the "original" plan for YorHa to end?
The infection was already around. If you read on the origins of a2 in the game it shows that she had to deal with killing android infected with it.
I think it's less a weaponised infection and more that the machine consciousness literally hacks into the androids.
The bots at the end mentioned their duties was to see the completion of Project YorHa (meaning to see that it comes to an end). How did they decide that this was the end if they didn't know about Adam and Eve?
They knew this was the end because they are overseeing the last yorha androids that are still operational and they all died.
The machines made Adam and Eve? Why? WTF are they made of? The story makes it seem like they've been around a while, so why did Adam get "birthed" in the desert? And why did another Adam/Eve come out of him when I killed him?
The whole coming out of adam thing I'm kinda iffy on really, but the pair was just a manifestation of the machine's interest in studying humanity. Also as a way to show that androids and machines are no different, given what we learnt about the black box.
The original "Forest King" was the first machine to have sentience? And his body parts gave all other machines sentience? Didn't look like a big enough robot to have enough parts to give away?
Dunno about the body parts thing (i think that's just the first kingdom's machines trying to create some mythology around their king) but the machine consciousness did deliberately break various parts of its consciousness so that it can study different evolutionary routes by studying individuals like pascal and the first king.
2E was designed as 9S's "executioner"? Seems like a defective mode.. why not just discontinue the 9S model? And since her primary role was to basically kill him when he got too close to the truth, why wasn't 2E with 9S from the beginning? Why were they split up (her in the air, him..on the ground-ish)? All the other combat models were destroyed at the beginning, did they *know* 2E would survive and rendezvous with 9S?
They didn't discontinue the 9s model is because he's really good at his job, but as said, he is too good at his job. So they get new information for every memory wipe cycle but have to make sure someone is there to memory wipe him. I think she wasn't there at the start because they don't have to worry about him at the start but yeah, i think that's just them meeting up, but he's off scanning a dangerous area. Guess it's a 2 stone 1 bird thing. They can scan and clear a dangerous area and get them to meet up at the same time.