Supreme Commander is Command and Conquer. It's an RTS, it has aliens, and it has the good guys trying to keep/restore justice, and the guys that want shit to be evil. Only difference is that it's like Warcraft, in that your commander is actually a unit that builds stuff, instead of things just popping out of the ground in Command and Conquer.
It's a good game though. I found it in a bargain bin at Ollie's (greatest cheap store ever) for 3 dollars. 3 dollars! I know its sequel is out (I tried it once), but I'm too lazy/poor to even think about getting it.