I have a theory. In the caves in Minecraft, you hear sounds. Angels, Planes, Trains. All to scare the player. BUT! Could those sounds also be echos of something that happened a long time ago? And then there is the bones. Maybe what happened was something attacked whoever was underground. Maybe the ancient builders. Imagine this, the ancient builders were getting ready to go to the Nether, or maybe before that. They created incredible technology. But, something attacked them. A monster much bigger than the builders. It roared at them and killing them one by one. The survivors fled to the Nether. And the monster slowly died of an unknown reason. Only the echos were left.
This might be the bones of that monster.