About halfway through the game, covenent rebels will start to rise. This is good, and bad. When you are doing the human levels (playing as Spartan-117), the covenent and covenent rebels will wipe each other, making the levels much easier. So, just find a spot where no one can hit/see you and watch the fight(you can make bets with your friends on who will win) until shooting stops altogether, then enter and blast the remaining hostiles. However, when you are doing the alien levels (playing as the arvitar) this makes the levels much harder to do, because you have two ene,ies. Fortunately, as far as I know so far there are no humans when you play the alien levels, with the exception of the dead human corpses that are taken over by the flood.