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The content of this page is meant to be viewed after you got Ending E!
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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. 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 and explanations of popular topics written by community members. While everything here is still a subjective opinion, it is a result of months worth of discussions and analysis heavily based on official sources rather than personal speculations.
Initial release: 19.11.2017
- 1 Why does 2Bs skirt explode when she self destructs ?
- 2 What happens to A2 after Ending [E]
- 3 Are №9/№2/A2 and 2B/9S the same?
- 4 ****
- 5 YoRHa Cycle
- 6 Machines/N2 role in YoRHa creation
- 7 What A2 does in the Ending [C]?
- 8 2B and 9S relationship
- 9 At which point in the game 9S learned the truth about 2E?
- 10 Which ending is canon?
- 11 Why 9S wanted to kill A2
- 12 When 9S got corrupted in Route C?
- 13 How 9S learns the truth about 2E
- 14 Weapon Stories
- 15 Song of a Broken World/ Weight of The World (Japanese)
- 16 Quicktravel and/or Death - What happens with Memory/Body?
- 17 Which Pascal decision is canon?
- 18 Who made androids?
- 19 Notes
Why does 2Bs skirt explode when she self destructs ?
Androids have specific parts of their clothes dedicated to radiating excess heat. In 2Bs case, the skirt is the piece of clothing used for that purpose, while for 9S it’s his shorts. This is why when they self destruct, those parts are destroyed from the immense heat the android releases.
Parts of 2B's skirt and 9S pants are used for heat radiation and wearing them allows heat to escape—Yoko Taro, NieR Automata Dinner Talk Show 
What happens to A2 after Ending [E]
Although she probably simply woke up before/after 2B, there is no real answer to this question. Yoko Taro has however stated that we are free to think as we like, leaving it up to personal interpretation.
With regards to all such speculation, you're absolutely free to think for yourself and assume whatever you please. I was told to give brief answers, so that's all I can say about this.
A2 was mentioned as being nearly fully repaired in one of the ciphered stories of the strategy guide, so it is likely that she woke up similarly to 2B.
The time when repairs are complete for 9S ... as well as 2B and A2 is near.—Strategy Guide/Ciphered Story 2 
Are №9/№2/A2 and 2B/9S the same?
While androids with the same model tend to share similar base personalities, their experiences and memories have shaped their self-consciousness data in different ways, resulting in each model being considered a separate “person”.
9S: I am who I am ... because of 2B ..
9S: I have a reason to live ... because of those memories ...—Precious Things 
Them being the same models would however allow them to swap said memory data between each other, though there has not been an example of this.
A2 and 2B have different self-consciousness data. Yes, it would be possible to transfer A2's memory data over to 2B. I was told to give brief answers, so that's all I can say about this.
Additionally, it appears that although they have the same number, according to Yoko Taro №9 and 9S are not even the same model.
Their names are different, which means they're totally different models.
According to the Project YoRHa story, YoRHa gets put in motion with only one ultimate goal in mind - creating a "god" for androids. There are no plans for loops or cycles - as №9, the person responsible for putting the project in motion says:
No.9: It was all just a ruse, telling everyone humans are still alive on the moon, just to give androids the will to fight!
No.9: But that little plan of his was incomplete.
No.9: There was a risk of information leaking out from that satellite base that was meant to manage the human server on the moon.
No.9: That's why I decided to rewrite his plan.
No.9: I rigged the thirteenth base to have a back door that'll open at a certain time.
No.9: The base'll be destroyed by an attack from machine lifeforms, at which point only the server on the moon will be left with transmission capabilities.
(No.9 slowly turns back, his tone sounding like he's just giving a speech.)
No.9: And so, I'll create a "god" on the face of the moon for us androids.—Project YoRHa 
This is further reinforced by the Timeline, which shows that the Bunker starts operating in 11940, and gets destroyed in 11945 - and that’s the one and only time this happens. The Project YoRHa also ends that year, with all data about it erased by the pods.
[Top Secret] YoRHa Disposal mentions that Backdoor is supposed to be opened when the time comes to switch to a newer androids generation, it is not instantly clear what does this mean since all of Project YoRHa data is being removed at the end. In truth, Backdoor was opened long time ago roughly at the same time as YoRHa was collecting data for its (YoRHa, not regular androids which don't even have official generations) new generation of models (which includes serial modes like 2B, 9S) from numbered prototypes (Number 2 (A2), Number 4, etc) - just as planned by Number 9 and written in the doc.
The Red Girls tell No2 and No4 that their mission was to gather data to create the next generation of androids, not necessarily to destroy the machine server.—YoRHa Musical Ver1.2 
Machines/N2 role in YoRHa creation
None. As evidenced in the Project YoRHa, YoRHa gets created “by androids, for androids”. Additionally, according to YoRHa Stage Play, N2 breaks into YoRHa servers during or shortly before Pearl Harbor, and only then discovers the truth about the project - if they didn’t know about it earlier, they couldn’t take any part in creating it.
Red Girl A: By hacking into your server, there is something interesting we’ve discovered.
Red Girl B: This is incredibly important, so be sure to listen well.
Red Girl A: The YoRHa squadron were created as experimental weapons.
Red Girl B: Everything was pre-planned by your headquarters, even your unplanned battles and dire circumstances.—YoRHa Stage Play 
What A2 does in the Ending [C]?
She transfers 9S’s virus to herself to cure him, and destroys all of the Ark data.
After many, many battles, 9S’s core data has been corrupted by the virus. “Alert: Severe virus corruption. Probability of successful deletion extremely low.” “...I think I know a way.” “...the idea under consideration is not recommended.” Though the pod’s words were stiff as always, they had a tinge of gentleness to them for the first time. A2 felt something funny bubbling up inside of her and gave the pod a mellow smile. “You’re not so bad, Pod. You know that?”
It felt like ages since the last time she truly smiled. How long has it been?
After transferring the virus from 9S’s core data, she approached the machine lifeform’s server. She heard the voice of children. The data that the machine lifeforms put into the ark with hopes for the future. Just who has the right to kill them? Who has the right to destroy their futures? A2 whispered words of apology.
Having lost everything, the tower crumbled away.
The sky is close from the top.
“I never quite realized...how beautiful this world is.”
The floor beneath her feet fell apart, and she felt her own consciousness fading.
“I’m coming, everyone...I’m...coming…”
Even to eyes that were stained crimson from the virus, the sky appeared endlessly blue and beautiful.'
2B and 9S relationship
Read: 2B and 9S Relationship
At which point in the game 9S learned the truth about 2E?
Which ending is canon?
With Yoko Taro it is never known which ending is canon since technically all of them are. Usually people call endings “canon” when they have a story continuation.
In the NieR Automata there are no alternative endings since Ending E is the final one you receive.
Is it C -> E or D -> E?
Strategy Guide Q&A mentions that in the Ending C Ark is also being launched but its content is empty.
Q26. What is it that was launched by the tower at the end? Is it a rocket?
That is the ark that the machine lifeforms launched towards the future. I guess you can call it a rocket in the sense that it uses propulsion to escape the earth’s atmosphere. The contents of the ark differ by route. In ending C, it’s empty (since all the machine lifeforms’ data that were supposed to be on there was destroyed), and in ending D it contains the data of machine lifeforms including Adam and the red girls.—Strategy Guide/Q&A with Yoko Taro 
August 6th: A structure from the "Tower" is launched into space.—Strategy Guide/Timeline 
2B (narration): I also heard about how the two of them destroyed some huge "Tower" that had been created by the machine lifeforms.2B (narration): The rubble from it is still scattered all throughout the city.—Farewell 
Since Ending E follows either Ending C or Ending D, both of them are possible. However Farewell also mentions a possibility of 9S moving inside the Ark, which in the game happens only in the Ending D. That said, 9S was still corrupted for a prolonged time in the Ending C and machines could’ve had time to invite him to the Ark (though this claim is not supported by anything).
In A Long Story, there is no Ending C presented and a story follows ending D with 9S choosing to stay.
Fun fact: All of the in-game decisions that were subsequently mentioned in side materials have additional cutscenes/sequences in the game.
Why 9S wanted to kill A2
The answer is rather obvious - because she killed 2B.
While 9S's reaction upon seeing 2B stabbed was understandable, why did he go on to hate A2 to the extent that he did?
Did it really seem like he actually hated her that much? I was told to give brief answers, so that's all I can say about this.
9S knew that 2B was infected. In the game 2B looks at 9S with normal eyes even though she looked at A2 with bright red eyes mere moments ago. This was probably made for a more dramatic effect. 9S wasn’t stupid and understood what happened - thus never in the route C 2B’s infection was mentioned even once despite Pods constantly exchanging information with each other.
Near the end of Route C, 9S motives became even more twisted since his obsession with 2B reached extreme levels coupled with the virus infection and a complete mental breakdown.
“Shut up. Shut up! SHUT UP! SHUT UP! Fine then...I’ll just destroy it...hehe...hahaha...if it all goes away, then it’ll solve everything!”
I wanted to be destroyed. I yearned to destroy.
Don’t look at me with the same face as hers! Don’t look at me, don’t look at me, don’t-!
Don’t look at me like that, he shouted from deep within his soul. I will not forgive you for having the same face as 2B. Or even carrying her sword, the same one… that day…
9S: You killed 2B.
That was the one thing, above all else, that could not be forgiven. Even if 2B had already been infected with the virus. Even if those eyes she used to look back at him were red.
9S: That’s all we need. For us to kill each other.
But perhaps he had fought A2 sometime in the past–it was just that 2B had deleted that memory. If that was the case, then A2 would know more about 2B than him. He began to fill with jealousy. Anyone and everything that knows more about 2B should just disappear.—A First Look at the NieR:Automata Novel – A Long Story 
When 9S got corrupted in Route C?
In the game and in A Long Story, 9S got visibly corrupted only after attaching 2B’s infected arm in the Tower. However, in Precious Things as well as in a Strategy Guide/Game Chapters Comments, it is mentioned that 9S got corrupted before 2B clone fight.
During 2B clone fight
9S was gradually being infected by the virus. He is no longer capable of rational thought. However, there is one piece of memory he managed to protect. His feelings towards her. Those days with her that he so cherished…—Precious Things 
Pod 042 (narration): Having lost a place to return to, unit 9S aimed for nothing more than the top of that "tower".
(9S is contaminated and is breathing roughly.)
Pod 042 (narration): The virus corrodes his body.
Pod 042 (narration): His thought process breaks down.
Since the virus was corroding his memories and taking them away - Soul Box is the most obvious place where it happened.
How 9S learns the truth about 2E
9S finds out 2B's true identity through deduction, he does not seem to retain his old memories.—Yoko Taro, NieR Automata Dinner Talk Show 
That said, in Soul Box as well as in flashbacks during A2 fight, 9S sees scenes from prolog of which he did not retain any memories of. But since this never was expended upon, we assume that it was either shown for the player or 9S received this data from Pods/Bunker/2B or it was just an oversight.
Read: Notable Weapon Stories
Song of a Broken World/ Weight of The World (Japanese)
Quicktravel and/or Death - What happens with Memory/Body?
Which Pascal decision is canon?
With Yoko Taro it is never known which decision is canon since technically all of them are. Usually, people call decisions “canon” when they have a story continuation.
Erasing his memory, according to the A Long Story.
The Machine Lifeform Peace faction, who Pascal used to be a central figure of, formally signs an armistice with the Army of Humanity—Strategy Guide/Timeline 
Fun fact: All of the in-game decisions that were subsequently mentioned in side materials have additional cutscenes/sequences in the game.
Who made androids?
Humans made regular androids (like Devola and Popola models) to oversee Project Gestalt (you can find more information about that in the first NieR game, NieR:Gestalt/Replicant).
After the project failure and humanity subsequent demise, the androids were left alone. Then the Earth got attacked by aliens. Some time during the war, androids created Project YoRHa, and by doing so, YoRHa androids.
- NieR Automata Dinner Talk Show
- Yoko Taro Q&A for Dengeki Playstation
- Strategy Guide/Ciphered Story 2
- Precious Things
- Project YoRHa
- YoRHa Musical – Notes and Spoilers
- YoRHa Stage Play
- Strategy Guide/Game Chapters Comments
- Strategy Guide/Q&A with Yoko Taro
- Strategy Guide/Timeline
- A First Look at the NieR:Automata Novel – A Long Story