This was caused by ultima WEAPON. it is where u first encounter it and when you do, it is pointing an energy power down at the crater, indicating that this is what it used to create the crater in the first place.

i think this may also occur to show how powerful ultima really is (though not really ) to perhaps deter you until you get stronger. when you can first fight it you're not necessarily that strong, so really any average joe could go and beat up ultima if they wanted.