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As far as
2. goes i believe they chose Mars because its a formerly unsettled planet, after realizing that all this time they have been emulating humans they might feel like this will help them get out of that since there wont be any human landmarks/relics to remind them. And at the same time they can get out of the eternal war with the androids and evolve in a different manner
Why Emil is in there is never clarified. As for why the machines have Emil like heads, it's never outright stated, but there's a hint at why (maybe) post game. What follows is a spoiler for the lvl 99 bonus fights.
Emil took the aliens on by himself and tore them a new ♥♥♥♥♥♥♥♥, seemingly prior to the creation of the machines. While he's ultimately unable to stop them, it's possible that his heavy resistance left a bit of a mark on the aliens, who modeled their army partially after him.
Alternatively, the creator of the games just really likes spherical heads.
They don't want to fight anymore, and they'd rather risk flying through space then obliterating the Androids and living in the ruins.
They weren't 'randomly' born. Adam and Eve were programs prior to being born as machine/androids. They're spawning when the character is there is either in response to the character, or contrived coincidence, which is a pretty wide spread narrative device and it seems silly to pick on this game for it.
The machine intelligence did not know humanity was dead at the start of the game. They learned it during the events of the game.
They aren't evil, they're just enjoying the fight a bit much. They're nice to you at the end of the game because they're done - They don't want to fight anymore. They've had enough, and they're not interested in blaming anyone for anything.
As far as them appearing in the desert, yes, it makes sense for the narrative to introduce them, but it doesn't make sense for them to appear in that way. Sure, they may have been programs before their birth, but that still doesn't explain why they would appear in the desert when their purpose is to be launched to another planet. I don't see a reason why they wouldn't just be born and kept in the tower as they seemingly are for their second appearance. Their presence in the first half of the game was inconsequential to their ultimate goal.
Also, I think you may be incorrect about the machines learning of humanity's extinction during the game. The cycle of destroying the androids has been continuing for centuries, and the machines were the ones allowing the androids to return each time. It doesn't make sense for the machines not to know. Can you point me to why you think they learned this mid-game?
They reach the end of the fight and they give up. They just don't have it in them to go the distance. There's nothing left to learn and there's nothing left to win - They finally see the fighting for what it is, pointless, and they're just done.
The player characters do the same, in a way - 9S abandons the fight for humanity, and even for 'revenge,' giving way to blind rage. And A2 just accepts that the world isn't the ♥♥♥♥ show she thought it was and accepts death (Until ending E).
They're goal wasn't to launch to another planet at that point of the game. You need to stop looking at this game like everyone's plans and actions are all to a single goal - Everyone's priorities change at a point in the game, as they learn more.
They learn about it during the game. That's why they go from 'Let's go interrogate some humans' to 'Humans are dead, lol.' If you can't accept that, then yes, the story is nonsensical ♥♥♥♥♥♥♥♥, and no amount of reasoning is going to save it.
Also, why would their names be Adam and Eve if their plan wasn't always to start a new population? I mean, they built a giant space cannon and an ark to fire out of it. Surely THAT didn't happen during the game's events.
This is a very ambitious and complex game. I think it is fair to suggest that maybe you should be open to the idea of plot holes, as well.
And all you've done is say 'nu hu, it doesn't make sense.'
If you don't believe that they were being honest throughout the game, and didn't change mid game, there's only one possible other option - They lied throughout the game and what happened at the end was their plan. And that's it. There's really nothing else to say or theorize and explain. They lied.
I'm not sure what possible other answer there could be. Either they were honest and their motives changed as their knowledge expanded, or they lied from the start, were ♥♥♥♥♥♥♥ you around from the beginning for a laugh, and there's really nothing to discuss.
Actually, the evidence is what happens. The characters tell you what they want, then the game shows you how they discovered that was impossible (The files they find while hacking android systems), and then the characters tell you what their doing now that their knowledge base has changed.
Your assumption seems to be that the characters are lying to you. In which case, I can firmly tell you that the game has no answers for you. No archives, no secret scenes, nothing. Just the lies that are told by the enemy for 40+ hours.
Because much like Western media is obsessed with pagan mythology and Asian aesthetics (And food these days), Japanese media is obsessed with Christian Symbolism and European mythology. It's why there's so many Japanese vampire stories and SS cosplayers and all that weird stuff.
Adam and Eve were sub-programs made to control and manage the machine network that gained a more 'perfect' image of humanity than most machines due to their supervisory role. They're named Adam and Eve because their the first close thing to humans the machine network has (Besides the Network itself). Just because their named after biblical figures doesn't mean they're going to perfectly emulate those characters, unless you think Marx frequently wrote papers in favor of socialism.
I've also stated that the machines couldn't have been ignorant of humanity's extinction because they are singularly responsible for the android's cycle. I don't think it's fair to ignore that.
I don't think it's unreasonable to suggest that the machines are lying to the main characters considering the android's continued existence is one big conspiracy to benefit the machines. It may also just be a plot hole.
What I do think is unreasonable to assume is that Adam and Eve were not named based on their ultimate purpose. Isn't it a pretty big coincidence that right after their birth, this ark-firing-space-cannon comes out of the ground and they end up on it? There is no way the machines thought of that idea during the game - it is such a huge undertaking.
The androids existed and had a system set up for Project Gestalt before the aliens were a factor at all. The machines had nothing to do with the YoRHa being created and the whole moon ruse. There's dialogue with Adam in the second fight with him talking about wanting to learn more about the humans but he can't because he can't get to them, as far as they knew at that point humans still existed. The machines seem to learn about all of it when the backdoor to the bunker was opened, which also wasn't something they planned they just took advantage of which the group that created YoRHa planned.
There's more information about the original group of androids in the first game and supplemental stuff and backstory for the first game in a book and audio CDs. You only see enough information in this game to tie it back to the first one but not necessarily explain the whole development of what happened leading up to the Gestalt/Replicant stuff. That project had the original androids created to manage it.
As for the ark that did seem to come about very quickly but Adam and Eve rapidly caused the machines as a whole to change throughout the game, maybe unrealistically quickly. But that makes a better video game than saying it took hundreds of years and trying to play through that.
There is simply a lot of ambiguity to the story. Many things are not explained that well, I'm sure there are even things that were meant to be explained but they've gone through the budget, etc.
Ending E is supposed to be initiated when all Black Boxes go dark, but if you pick it from chapter select, it has a cutscene from Ending C, in which 9S presumably survives. This is not to mention the YoRHa units in the desert, and other scanner models such as 4S.
At the end of the YoRHa stage play, the Commander wonders if the destruction of YoRHa generations (A2's squad) is really necessary to iterate and evolve (creating 2B and 9S's generation), and if that is the inevitable goal of humanity, as if she believes that humanity still exists. She doesn't have any illusions about the state of humanity in NieR:Automata.
Furthermore, the Machines have been rooting around in the YoRHa servers since at least the YoRHa stage play (that is, the assault that A2 was part of). For whatever reason they don't destroy the Bunker until route C/D of NieR:Automata.
The reason that A2 knows that she was betrayed by Command is because the machines specifically lay it out for her, telling her that her mission was doomed from the start, and every single one of their "failures" and deaths was planned by Command. The mission was actually a failure in that A2 wasn't supposed to survive (or any of the resistance members she met for that matter). The machines actually specifically shut down the warning signal in the Bunker to keep Command from knowing that A2 has not been destroyed at the time.
Still, the machines decide to decimate the current YoRHa generation at the start of route C/D and then subsequently lose interest in fighting altogether despite the fact that they believe that their reason for living is fighting the androids, so much so that the specifically sabotage themselves so they can never fully eliminate androids.
So yeah...