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FextraBot

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Creepy little *****ers
If I was a machine life-form, I'd want to be a little girl too.
A possible shout-out to the route A final boss from Drakengard.
Her clothing is definitely similar to Manah but I think it's just a visual reference without deep meaning.
There is also the voice shift, that is another similarity.
They say that time has little meaning to them, so is there a possibility, throught some sort of transcendence, of Yoko Taro wrapping it back to Drakengard lore?

DarkZazin

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I want to know every single locations we can see her/them on. I mean, I have seen her on two locations in the background while I was talking to a NPC or interacting with something. I do NOT remember where I saw her the first time but the second was inside the bunker. Anyone knows more locations and the story why she is there?
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Fallenangel700

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First time I saw one, was in the bunker just before 9S got into the flight unit to go help 2B at the end of route B. Almost thought I imagined it.
2nd time was at the end of route B, but those were pretty hard to miss.
Saw one in the alien mothership while 2B and 9S were talking with Adamn and Eve.
They were in the background of 9S Route B leaving Bunkers Hanger and after killing Eve saw 2 of them.
She's in the 9S (Route B) cutscene where Adam and Eve teleport away from the Alien ship after they fight 2B and 9S
https://youtu.be/bLye5K_wIOs?t=2h34m39s
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Fallenangel700

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Whoa. Blink and you miss it.
https://www.dropbox.com/s/odugstpexaye8sb/TheGirlsofTheTower-TheUnexplainedStoryofNieRAutomata-1.pdf?dl=0
so this is one of the best theories concerning the red girl which would shower her true importance to the story and project yorha and includes the reason why she was in those 2 locations in the 9s route.
If this is true then we totally underestimated yoko taro's true genius in the story writing of nier:automata
too bad this is all false theory
All of that document is *******. Watch Yoko Taro's stageplay for details on N2.
When all I had was the information in the game from my playthrough, the best sense could make of it was a theory similar to the one in your link.

That said, additional materials from outside the game seem to contradict it.

A shame really as that theory makes more sense than the official story, especially for things like the Bunker having a backdoor that the machines could use to destroy it.
she also appears when you are leaving the Bunker after everyone gets virus, I think in both A and B routes
Thats route C
she do appear during route B, when 9S has to return to earth after the fight with Adam.