One of the main hang-ups connecting the ending of NieR with NieR:Automata, its distant sequel, has been the fact that… Well, humanity should be extinct. Completely and utterly gone. Dead.

Whether he realized it or not, by offing the Shadowlord, Nier essentially doomed all of humanity. Or did he…?

Let’s stop there for a quick moment and take a look at some important plot-points for the YoRHa stage play and NieR:Automata:

• 5012 – Before witnessing aliens invade, Emil mentions wondering where humans have gone since he hasn’t seen them around in a while. This proves that some humans actually *did* survive the initial failure of the Gestalt Project.
  [ NieR Replicant Drama CD, Disc 2, Track 3: “The Space War” ]
• The aliens create “bio-machines” as proxies to fight the humans. War between the aliens/bio-machines and humanity continues for thousands of years.
• 11939 – The 14th Machine War begins. Humanity is forced into exile on the Moon. Just like the aliens who created the bio-machines, humanity needed to create battle androids to effectively fight and reclaim the planet.

But… wait a minute. How can there be humans in this storyline if they all went extinct after the end of NieR?

Well, a clue about this might have been hiding in plain sight all along, on page 167 of GRIMOIRE NieR:

Here’s my translation:

The Failure of the “Gestalt Project” and the World Thereafter…

The “Gestalt Project” progressed smoothly despite considerable uncertainty. Even so, the project was deemed a failure when a fatal defect caused Gestalts to relapse while Replicants mysteriously obtained self-awareness and a will of their own.

With the death of Gestalt Nier, the “Original Gestalt”, all “Gestalts” would eventually relapse and die. Since Replicants lacked the ability to reproduce, it was imperative to copy the Gestalt data in order to reconstruct their bodies. Otherwise, humanity would perish with this current generation.

After Replicant Nier defeated Gestalt Nier, it was unclear whether he was aware of his decision to save Yonah would inadvertently doom the entire world. Not far into the near future, the last of the human race would disappear from the face of the planet… unless a new “Original Gestalt” could be found…

Even if the Gestalt Project: Plan A involving the Shadowlord failed, there’s still a slim possibility that a Plan B could succeed if a NEW “Original Gestalt” was found.

The main problem with NieR is that we’re lead to believe, or rather assume, that the Replicants and Shades that Nier comes across are the only ones still in existence. This could be a vary inaccurate assumption to make, given the size and scope of the whole world.

I would bet that the people at the Hamelin Organization, the secret government agency that’s behind the Gestalt Project, would have had some sort of contingency plan in case Plan A failed. I’m confident they would have another “ace” or two up their sleeve.