Bronzespooky

My friend and I are playing through this game at the same time and we have noticed that I am not getting significant story line features that he has been subjected to. For example in Mt. Moon when team rocket makes their appearance he engaged in a battle with them while for me they simply fled. I think this is detrimental to my play though of this game because i'm not getting what was intended. Which makes me wonder if there is a solution to my problem.