If you've ever played a first person shooter you'll know that most of the time they follow a strict plot through strict areas of their world. Each time you play the game it will be exactly the same as the last.
Whereas if you play an RPG, it has what the games industry refers to as an Open World. This means you can choose where you want to go and to a certain extent, what you want to do. This has been done in a 3rd person shooter before (focusing around criminals) so what would make my idea unique is having it based around special forces.
You could choose what suspected enemy bases and safe houses you want to raid and when you want to raid them. But you can't just go raiding wherever because if you raid a incorrect house within earshot of the real base, they will be alerted and will pack up shop ASAP. When you are not on a mission you could be an undercover agent trying to infiltrate the enemies system to find out more information about where they are located. If you're good enough at going undercover you could even become a double agent, tricking the enemy into thinking you are on their team.
As the 'goodies' you could set up your own bases that would from time to time be raided by the enemies. The game would therefore have an element of strategy (where to set up base, when to move etc). As you defeat more enemies, the government could give you more funds to set up bigger bases with more ammo stocked and more soldiers to help you.