Ok I have gone through all the endings and even read the stage play and I am still confused as to what the hell was going on here. Spoilers Below:
Ok so 2B was designed as 2E to kill off 9S anytime he finds out the truth of what was going on. Just how many times did she do that and under what circumstances? Was there prior wars/missions they went through to end that way? I'm not even sure what the point of that was since they could have just deleted 9S' memory or not even bother creating 9S to begin with (lot of plot holes here).
A2 was part of a "suicide squad" of Yorha sent in the last war right? Any more information on her backstory or what she was doing? She's just like wandering around aimlessly until 2B needed her help with the virus??
And even though the Commander/A2 mentioned there was a human server on the moon with human genome, 9S claimed that was a lie and there was no server. Which is the truth? And why did they even bother to hide this from androids to begin with? They are all following programs right? Who created the Yorha and what purpose did it serve to fight and die like puppets when theres no humans left? Why go through all the effort to fight when they only are programmed to die off like with the Bunker back door for the virus?
And in Ending E when the Pods are rebuilding 2b, 9s, a2 what is the goal for this? Are they trying to restart everything back to the beginning of Automata and get every android and machine to refight each other or something? I'm not quite sure how thats possible unless they have a new Bunker, Commander, Operator, etc in a spare closet somewhere. Sorry for the length but what was the point of everything? Is this all just programming left over from the human inventors of the androids with the death of Yorha or some other purpose? Why even create and kill off the Yorha like the Pods said in the Ending the project was complete by killing all Yorha. What was the goal of this "project"? What does killing Yorha accomplish?