I just finished Assassins creed. And im confused. Who are the bad guys?

You spend the whole game slaying these templars who are supposed to be the bad guys. Then you find out your master is also evil. So, the templars you killed..were they actually innocent, and the master was the only bad guy, or were they all evil? And exactly how does this tie in with Desmond and his captors? Are his captors templars? i need clarification please.