It was something done out of necessity, in a desperate bid to prevent humanity’s extinction, with quite literally no other choice.
What remains of humanity has been forced into a single underground city by an invasion of incredibly hostile machines known as Raptures (no, it's not really known yet where they come from). A significant amount of the male population was wiped out trying to hold off the Raptures, leading to the necessity for women to also fight. A standard human is largely incapable of wielding the kind of weapons needed defeat a rapture, which lead to the creation of a process by which the human body can be wholly transformed by special nanomachines called NYMPH to give them the capability to oppose the Raptures. This process also wipes the memory of the individual the vast majority of the time, turning them into a more or less blank slate. Nymph also allows them to suppress pain, emotions, memories, and trauma, as well as sustaining the brain in the event of bodily destruction.
It's one of those "ship of Theseus" situations where only really the brain is still technically human, and even situations where the Nikke is forced to face this really can lead to a complete mental breakdown on her part, requiring a complete mind reset. And what happens when people in high stress situations are forced to live alongside something that looks for all intents and purposes like you but very much isn't? Racism and xenophobia.
For a game which advertises staring at an anime girl's ass the whole time, there's actually a really well put together story, world, lore, and characters. And music. Good god the soundtrack fucking slaps.