Odds are good the woman in the mask is or is somehow connected to the Kyuubi no Yoko, aka Ninetails. If you're at all familiar with Eastern culture, you should be able to tell that that makes her Bad News.
It's impossible to be sure though, as Ammy kills the Ninetails in-game and Mashadar has confirmed it really did happen. It's possible that it's a new one, a reincarnation of the old one, or something completely different using her telltale symbols as a disguise, and there's really no way to tell until it comes up in-story.
As for the ark, here's the short version:
Way back when, there was a group of people known as the "Moon People" who, appropriately, lived on the moon. Then the demons came and started killing them all. They weren't able to fight, so they fled for the Earth on a spaceship they called an ark. Unbeknownst to them, however, this ark had been infiltrated by the demons and by the time the ark landed on Earth, all but one of the refugees had been slain. Then the demons came pouring out of the ark and that's how they showed up on Earth.