Hmmm
I'm spoiling because it may happen in the epilogue, who knows.
I think Nayuta's plan worked in the end. The epilogue may be completely related to DEEP and Nayuta's connection to the Queen. At some point Nayuta, in the present, will talk with Mirror again, and she will reveal that she "won". How? By ruining Mirror's plan. She wanted Marian to be the Queen, and thanks to Nayuta that plan got slowed a lot. Not only that but the Goddess herself came back, although the Queen taking her body is a big problem, it's a problem that can be solved at least. Nayuta took a major gamble there.
Now the Why Nayuta did all of this...is because she knows DEEP is behind this. Mirror is related to them. And Nayuta knowsthat they are the absolute evil that has to be stopped no matter what, and for that reason she will do everything it takes to do that, even if it means putting the whole world at risk. Then Rose will put her blade in Nayuta's throat, because Scarlet got heavily damage. Nayuta will answer that for those who came from the Depths (DEEP duh) Life and Death is nothing. They are beyond that. They are the Alpha and the Omega after all. All of them will be healed in time. But for now she has to keep her powers in secret or some shit like that.

In any case, I'm coping because I really want to see and know more about Nayuta's connection to DEEP, she went to some really weird extents to track (like using Eden, using clones, collect information around the world) and eventually kill the Queen too, and her saying "Finally" after the Queen died really makes me believe she has some kind of connection with her