Well, that was... something, I'm having Evangelion PTSD here.
It begins as something somewhat interesting, then it becomes a kind of weird and confusing, and end on a big wtf.
And well, it's actually Evangelion, isn't it?
Divine monsters coming out of nowhere to kill humans, a socially awkward human with almost zero confidence trying to save the world.
Using a divine entity to kill the bad divine entities.
The lesbian not so subtle subtext.
The prodigy child causing the apocalypse by deifying all humans into a single apocalyptic lifeform.
But ironically enough for a lesbian oriented story, there is a huge lack of vaginas compared to Evangelion ending.