During route B, in one of the additional cutscenes, the narrator (I'm not sure if this is 9S, so I will stick with "narrator") mentions a
god, who came from volcano, and taught machines about emotions.
What is this about? Most of those cutscenes are telling us a story of machines gaining self-awareness, but this particular part is not exactly clear.
Currently, I have only one theory:
Appearance of god from volcano is symbolic description of server destruction in Mt. Ka'ala during Pearl Harbor Descent. After this, there was no central hub to control all machines, so they've started to become sentient.
If there more solid theories or facts, I would like to hear them.
Best Answer
Apparently, it is a direct reference to a novella titled "The Fire of Prometheus", written by the director of the Nier games, Yoko Taro. The entire story can be found here.
The novella is a relatively short read, but to summarize:
Yoko Taro himself made the connection during a 50 question interview he did for NieR: Automata. The entire transcript is provided in this reddit thread.
The relevant part is here: