But the biggest changes come with Sam's moral choices. As a double agent, Sam's orders are frequently in conflict; the government might order him to ensure a man's safety, for example, while the terrorists will in no uncertain terms demand the guy's head on a platter. Your choice determines the flow of the story and which side missions you're given, as well as each organization's trust in Sam. Earning the bad guys' trust will usually net Sam some better equipment, but don't earn too much or the government will get suspicious and pull the plug on the mission.