I stumbled across a really interesting anime which starts out with two young men exploring the ruins floating in the sky, looking for relics of the ancient heroes. They stumbled across a girl who passed out and, when she woke up, refused to tell them who she was.
They brought her back to the village, only to be explained that she couldn't see the lead character's friend or any of the villagers as they were "spirits", and the lead character was only able to see them because, having grown up there, he has become accustomed to their "presence".
The girl ended up attracting a monster, which broke through the barrier protecting the village, forcing the villagers to defend themselves.
That's as much as I can remember, unfortunately. Hopefully this is enough information.