Ok so I admit I held off from playing through ending E 'til now even though I got the others a while back. (Took out my whole save for the moment, just didn't have the heart to say no. xP)
But yeah, after beating it, that was the game's most rousing, heartwarming stretch of play. Even if it did take quiiite some time, from the first moment I died and on it just gradually became more and more absorbing, from seeing the taunting prompts on the screen to the steadily increasing number of messages floating in the background, and then dying again and again until, finally, you go FUSION mode and..that chorus. That music. That song!!
That alone could have just set this game's OST of the year status for me lol. Exemplifies how the dynamically cued music seamlessly transitions and keeps things fresh...while also leaving the player an emotional wreck. The way it shifted from English and Japanese was also brilliant. With the choral backing accompanying... just... what a powerful moment. A message of unity and anti-nihilism well sent.
The logic virus targets all androids, some of the Resistance characters get infected in the stage play that's a prequel to the game and it's also mentioned in the Pearl Harbor logs. Although the "backdoor" only applied to androids that synced with the Bunker.
Speaking of the logic virus it sure has parallels to Red Eye. Plus it's crazy how randomly strong Adam and Eve (the latter with dat Cult tattoo) are. Like, supernaturally so?! With the hints of Watcher involvement and etc. it definitely makes you wonder how they could have possibly meddled with this whole situation...but hey, Nier 3 will come in time.
I don't think Yorha literally repeats. The war does, and many machines/androids who have fought many times are rebuilt/repurposed, but I think this is the one and only war where Yorha was a factor.
There's only one generation of Yorha androids besides the prototype run that A2 is the last member of. If the Yorha cycle literally repeated, surely 1. the non-Yorha androids on Earth would instantly know what was up and 2. wouldn't Yorha spec androids be all over the place/not a "new" design? If Yorha and the machine network were the only characters in play, I think the literal repeating test/cycle would make more sense, but there's a whole world of androids out there who would surely notice that Yorha kept getting built up and torn down. The logic virus only targets Yorha if I remember correctly, so it's not like it's an android-wide apocalyptic event.
When the Pods refer to the possibility that "everything could happen the same way again," I think they're referring to the cycle of violence and war that has happened so many times previously, not a literal repeating of the same cycle. I could be wrong though, but right now I'm leaning more towards the cycle being figurative more than literal.
EDIT - I would submit that there is evidence for this interpretation in the fact that their recorded date continues to tick up from the original Nier's - time is still marching forward and everyone is aware of it.
I also read that androids' main goal will be to actually become as human as possible, thus filling that hole they left behind. The androids are that desperate for meaning that they needed the deception...but with our party of three still kicking even after learning of the whole thing, maybe they could finally learn to live for themselves, and together.