Asklemmy

You kinda play with reincarnations of Adam and Eve but original Eve was kind of Adam's mom. Current Adam has a lot of trauma he tries to shut away with different personalities but then the ghost of his previous incarnation takes over his father's body to try to push the traumatized personality out. Eventually you discover a kid on a lab who comes to life in your presence and she tells you it was an even older incarnation of Adam who created her artificially based on Eve because nobody could have natural kids anymore at that time but that didn't really wipe humans out either. And all through the game some sort of AI with the personality of some very old folks had been spying on you through your save files. In the end current Adam and Eve fall out of the sky naked but inside a giant robot, with all your friends watching you from a distance because they can't fly since your actions made every other giant robot stop working, except for yours.