Well, that leaves sci-fi team-vs-world. My plot still qualifies, sans the later stuff with superpowers. Anything up to driving the first batch of aliens off the planet will work, with the arriving fleets of other races as a sequel hook.
Start out with modern military fighting a hopeless struggle to keep the aliens out, continue with the Resistance operations against the invaders, finish with a complex assault on the aliens using their own weaponry.
If you want, you can attempt to incorporate the Battle Mastery technique from Banpresto's SRW series. Basically, dynamic difficulty based on completion of optional goals, with rewards thrown in. So, if you storm through the beginning of the mission and arrive before a certain time, you'll have a chance to, for example, avert or tamper with the launching of some missiles. The reward will be armored backup or advanced hardware in some future mission from whatever area you saved, the difficulty will be that for one, you'll still have to deal with the original goal (and from a less advantageous position), and you'll see an increase in the number of guards around such places in the future.
Add a plot fork or two to get the player to feel like he's having more influence on the events than is actually possible. Say, the player character attends a meeting that discusses two parts of the same operation, and is given a choice to volunteer for one or the other. Both would succeed and the plot will return to the same stream afterwards, but there would, again, have to be some future repercussions for choosing either route. So, if you choose to assault the alien labs, you can complete an optional goal and get yourself an advanced gun a little earlier in the game, but if you don't choose to attack their airfields instead, you won't have friendly air support in a future mission, which you could have earned in that branch.