From what I've deduced from playing the game, the reason women can't get pregnant the normal way is probably something like this: The Dark Fairies hate all men but want the women to continue, so after they wiped out "all" men, then used magic to change how women get pregnant, allowing them to get impregnated only through a ritual (probably with another woman somehow fertilizing the egg), but this only allows them to give birth to girls (since women don't have a Y chromosome, the offspring from 2 women won't have it either).
My believe that sometime during the main story, the MC will somehow learn to undo the magic that the Dark Fairies used (hopefully on only a few women at a time, and not all at once), thus allowing him to impregnate them.
