I feel like Eris is bad. Corrupted by the hive (she's turning into one) she has us destroy his soul, or the crystal he's in to release his soul. That way he can take form in the raid. I believe the giant Skelton in the wakening is how large crota was. When you fight him in the raid before he appears you see a large fire form of his face. I think that's how big he once was. The crota you fight is just a ghostly figure. Again this is just me stretching while I wait for bungie to up the story.