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[PrejudiceSucks]

If you hit them in the head then you might be alright, but the best way to tackle them if all you have is rifles is to surround them (pretty much) and then shoot them so many times that they get stunned (as every shot stuns a creature a little bit).

Then you should just take them into your Skyranger and just run away unless you have any real desire to fight more than one of them :P.

Of course, to kill off Muton Commanders when you have rifles (God forbid!) then you need to utterly surround them, throw smokes grenades at them (when they're in a room) and then just fire wildly into it until you hear it drop.

Or you could always just throw explosives at them, or set them on fire before you get lasers.