We have a Lore FAQ page. If you have Story/Lore related questions - make sure to check it out!
Lore FAQ
The content of this page is provided as-is. While you are free to disagree and write about it in this /u/wesStyle, we reserve a right to only correct factual mistakes.
Following content might dramatically change your views on cetain topics. You have been warned.
NieR Automata has a very complex, multilayered plot and it is normal to have questions after finishing the game. Yoko Taro is known to present things vaguely so that players could find answers themselves. It is especially true about the base game story.
However, Yoko Taro also likes to publish a lot of various Side Materials after the game to shed some light and comment on different topics as well as extend the lore.
On this page, you can find a list of answers to frequently asked questions as well as some explanations on popular topics.
While everything here is still a subjective opinion, it is a result of months worth of discussions and analysis which is heavily based on official sources rahter than personal speculations.
That said, you are highly encouraged to read everything yourself and make you own conclusions.