Turns out the aliens had died centuries ago, which explains the widespread shift in machine behaviour. Fighting a perpetual war at the whims of creators long since perished; left only to contemplate the meaning for why they even fight. Separated from the network and given the opportunity to act on their own free will.
It's here you reconvene with twins born amidst the machine orgy. They talk about humanity and vow to kill them. While this exposition is happening you fight the twins on a 2D plane, one on one. Like before the fight is more annoying than it is hard as they keep teleporting around and going invulnerable.
Following that I was finally given access to the transporters allowing me to fast travel across the map. This spurred me on to continue working through side quests and I believe to have hit the wall as to how far I can progress without strenuous effort. One side quest in particular "11b memento" featured an ambiguous conclusion. Said quest involved finding the body of a deceased android designated 11B and to bring back whatever remains were left as mementos.
At the end of the quest you are provided a choice to tell 16D about 11B's planned desertion or choose to withhold the truth. If you decide not to share her plan, then 16D will confess she was in a relationship with 11B and that she'll convert into a combat model in order to avenge her. However, should you tell her the truth; she proceeds to laugh and speak mockingly of 11B's death. Revealing that she had been continuously abused and with her passing she was now free to devote herself to work.
On picking either decision, 16D will reward you with a [Melee Defence 6+] chip and say "I don't have a reason to protect myself anyone..." carrying heavy implications to the severe extent of her abuse from 11B. This contradicts the outcome of not telling her; in which she talks about how 11Bs desire to protect her seemed "romantic at the time" and even going so far as to convert herself. From what I gather the combat models are typically seen as superior and this tends to manifest into an inferiority complex within many defensive models. Perhaps it's why if you don't tell 16D the truth she speaks so highly of 11B compared to if you do, as by maintaining the belief that she was inferior she could somehow justify her suffering under the pretence of it being the status
quo. Her choice to convert models could be construed as attempting to escape this abuse, she wouldn't be viewed as inferior and thus not risk being abused or used as a disposable shield.
But when confronted by the reality of 11Bs death she disregards this notion entirely and lets out their true feelings unburdened from a hierarchy that coerced her into thinking otherwise - in this scenario she chooses not to convert to a combat model as she no longer has to believe those units are infallible. 11B is gone, she doesn't need to protect herself anymore.
Of course there is room to speculate alternative possibilities, for instance perhaps their relationship was genuine. The disparate hierarchy narrative can also by applied here, 16Ds affections towards 11B may have resulted in her overextending herself and sustaining far more abuse then she needed to. When asking the player to seek out 11Bs belongings - she isn't sure how to process her grief being unfamiliar with the experience of losing someone precious. What you tell her in the end influences how that emotion is handled. In not telling her, that image remains intact and decides to go off and try get revenge; leaving behind her defensive chip since if she can't find peace in avenging 11Bs death than she has no other reason to live at all, possibly suicidal unable to cope with the loss. You betray that image when revealing the truth and unable to accept it, 16D reevaluates all of her prior experience and attempts to frame it negativity since she has nowhere else to direct her emotions. She decides then to occupy herself in work to avoid thinking about 11B and move on.
I could just be delving far too deep into a minor side quest and looking for depth where there isn't, but this kind of moral dilemma and thought provoking subtext were frequently touted as proof Nier: Automata was something more. So I tried my best to engage with it.
