Well, look who ignored my uncomfortable comment just like I predicted!
What? How does holding the quarians over the fire and forcing them to unconditionally accept domination by synthetics equate to "getting along just fine"? Sounds pretty teeth clenching to me, at least for one side of the equation. Han'Gerrel doesn't stop trying to eliminate the geth because he has a change of heart, realizes the error of his ways and goes to give Legion a big hug. He realizes that he is defeated upon being informed of the geth's reacquisition of Reaper upgrades, and is being given a choice between submission or extinction. Much like Saren before him, or the geth earlier in the war when faced with the Faustian bargain of submission to Reaper control for "survival" or destruction by the quarians, he chooses the former.
Domination? What domination? The geth and the quarians cooperate with each other. The geth are doing what they were originally designed: helping the quarians - but out of their own will, not because they are forced to do so. And those who have geth installed into their suits? They are volunteers. Calling this domination is like speaking about the Council's subjugation of human while you are playing the first human Spectre.
Also, Gerrel is still dedicated to his suicide attack upon hearing the geth's return to full force.
Negative! We can win this war now! Keep firing!
It is the authority of Admiral Tali'Zorah and Zaal'Koris and Shepard's words are what actually convince him.
The geth are about to return to full strength. If you keep attacking, they'll wipe you out.
Your entire history is you trying to kill the geth. You forced them to rebel. You forced them to ally with the Reapers.
The geth don't want to fight you. If you can believe that just for one minute, this war will be over.
You have a choice. Please. Keelah se'lai.
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(Tali has comparatively little issue destroying Legion and apparently couldn't give two shіts about any other geth judging by comments, and Legion will genocide Tali's species in its pursuit of code upgrades without even considering other options).
According to Legion themselves (itself? himself?), they considered other options and found none.
Admiral Raan states that the quarian and geth forces are kept completely segregated to avoid the huge likelihood of violent incidents. If both the geth and quarians survive the war (which can only happen with the Control ending, and no the altered....things in the green ending are no longer geth and quarians) their slides show them completely segregated (with quarians still in their suits despite Tali's lofty prediction that within a few years they wouldn't be needed with geth "help") suggesting that the nascent "cooperation" was short lived, with only the threat of Galactic Dick-tater Shepard VI keeping the "peace". In the initial script, Admiral Xen was supposed to even go rouge after Rannoch and start reprogramming geth to self destruct, causing a huge diplomatic mess and further driving this point of continued unrest home. The files are even still on the disc, and some have accessed them and gotten the cutscenes describing this event in youtube videos.
Some degree or separation between organic species is common. Colonization is rarely a joint-species effort, and even the Citadel has its asari, turian, salarian, etc. wards. Why would it be different between organics and synthetics? And if there are a smaller number quarian and geth living in the other's cities, you can hardly account for demographic distribution of minorities in a single picture. And they are living in separate cities, not the bombed-out remains of said cities. This shows that coexistence is possible, even if won't necessarily result in a utopia.
Xen's actions only prove my point in the earlier post: it's not that no organics can cooperate with synthetics, but that those few that refuse to do so try and destroy both synthetics and those organics who do.
The only reason they work together at all is because the quarians are rendered incapable of destroying or controlling the geth once the latter acquires Reaper technology, and the geth (logical machines that they are) would rather have quarian assistance against a more dangerous enemy in the short term. Greater causes are all good and well, until those causes cease to exist and everyone remembers the original conflict. Remember when the United States and the Soviet Union became best friends forever after helping each other defeat the Nazis? No one does. Natural enemies are still enemies, and the cycle that has happened thousands of times over billions of years will repeat itself without the fundamental changes brought about by the endings. Nothing about the geth forcibly subjugating the quarians suggests the cessation of conflict, or does anything to refute the Catalyst's logic. That's a patently silly interpretation of the events presented.
But that conflict doesn't ended with a nuclear exchange. It ended when Gorbachev, leader of the SU, introduced such American (well, with a big asterisk) ideas such as free market, democratic elections and freedom of expression. It was the reaching of a (partial) consensus that resolved (partially) this conflict of ideas that you consider only solvable by violence.
Yes, it wasn't a smooth process. Washing a mud-caked wound out with disinfectant is painful. But it's better than lopping off the limb it's on.