Hehehe, actually in Soldier of Fortune 2, they've taken that element and worked on it very well. If you disobey orders from a Commanding Officer too many times, or take out one the Special Forces guys your working with in many of the missions, you'll be hunted down and taken out. Thats something that is very cool. in all reality though, why would you want to shoot one of your own men ??
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Blessed be the Lord my strength, which teacheth my hands to War and my fingers to fight.