* So, Original Nier becomes a perfect Gestalt but Yonah does not. The originals die, but the "copies" live on.
* In order to coerce the Gestalt Nier (Shadowlord) into helping Hamelin refine the process of soul transfer, they store Yonah's body in suspended animation until such time has passed that WCS is finally over.
* Work progresses using Gestalt Nier's DNA to enhance the process of saving the surviving humans by creating compatible replicants, but ultimately this sows the seeds of destruction.
* Colonies of Replicants are created with basic synthetic personalities to prepare for the day when the human race (soon to be extinct) is ready for rebirth.
* Gestalts are immortal (or at least extremely long lived) but Replicants are sterile and mortal. For this reason Devola and Popola are androids used to preside over a cycle of death and rebirth until the time is right.
* Over time however the Replicants develop real souls and personalities, leading to the middle-ages like existence we see in the game. The inference I guess is original Nier's DNA is to blame.
* It seems like some kind of psychic link exists between all gestalts created with original Nier's DNA and his gestalt (The Shadowlord). His rage over his inability to save Yonah (this is building over thousands of years remember) is causing Gestalts (shades) to "relapse" - lose self and attack replicants, and for the corresponding replicants to sicken with the terminal disease known as the Black Scrawl.
* Popola and Devola at least suspect this is the case, but are unable to act on it as they are simple androids following their millennia old programming. This is the Law Of Robotics writ large once more ; ;
* In response to this building crisis they activate Nier's replicant and set him on a path to reunite the grimoires and bring about the reunification as soon as possible.
* However when replicant Nier releases Weiss, he damages the book causing him to lose his memory and purpose. It seems like the personality we know as Weiss in the game is more like the original (unwilling) human used in its creation, than the tool of destiny they intend.
* Seeing this last hope to save Yonah fail, the Shadowlord snaps and takes replicant Yonah anyway - forcefully reimplanting her soul on top of the existing one at his castle/lab.
* In the years following her abduction Replicant Nier becomes unexpectedly powerful and the spread of "relapse" and black scrawl cases spirals out of control... thus the stage is set for the destruction of all.
* Yes folks, this is Cavia writing and WE'RE ALL GOING TO DIE TRAGICALLY!
* When Replicant Nier kills the Shadowlord, Popola and Devola the mechanisms that have been keeping the human race alive through cyclic rebirth -both replicant and gestalt- is basically destroyed. The flawed gestalts are doomed to lose their selves and attack the remaining replicants, and as the replicants cannot reproduce when this generation ends, so does humanity.
* So yeah, there is no happy ending.