You are Watanuki. A part of him. It's a little hard to explain, so bear with me.
Some games, the ones run by Phedonra, involve exploring the "heart." A literal manifestation of it -- everything that makes a person who they are. They can be forests, cities, a building full of rooms, all symbols in some way. Some days ago, we were shown the history of this place, so Watanuki knows all about Ter Feramis. He kept those memories and that person somewhere in his heart.
But Watanuki... has a lot of trouble with some things. He has difficulty believing he ought to be alive, that he makes others happy, that he has as purpose. That he has a right to exist and he's wanted.
That part of him in his heart was confronted, and things went very wrong. He erased someone he loved, and in doing so erased almost his whole heart.
Everything but two parts is destroyed. You're what's left, with a little urging. That's why you're so confused, why there's probably a lot of gaps and things you don't understand.