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Within the world of Project Renegade, there are going to be pre-ordained missions set up by the different factions in order for them to accomplish their goals. Your character has the option to participate in these missions or not. They also have the option to complete the mission as they see fit.
For example, if a Rebel faction wants to cut off a government supply line, you could blow up a bridge along the supply route. You could also hijack the convoy and deliver the supplies to the rebels, any way you see fit to complete a mission.

Another option will be planning your own missions throughout the game. Lets say you know that a leading rebel official is going to make a public appearance in a few days, you as a government soldier could do the recon, plan the operation, and potentially assisinate the rebel leader. This would change the course of the game as you have just cut off the head of a rebel faction. These sort of missions would be yours to plan, and execute. the game however will not automatically allow you freely conduct your own ops. Let us say you attempt to assisinate that rebel figure by attaching a bomb to his motorcade. One of his security guards could in effect find the bomb and then spoil your op and might end in your death. So it is up to you if you plan your own mission based on naturally occuring events in the game, to make sure you plan every detail and tie up every loose end.