Cool idea. I assume both sides will have high tech arsenal and you will discover and research new alien items to help you create interesting new weapons. Blaster Bombs won't come into the picture on the Aliens side, because they don't want to pollute their world, but close to the end, with no choice, they will use them.
So what would be the final goal? After researching plots, you learn that you need to find the entrance into the deep underworld city by creating bases with adv. radar all over the planet. Once you find the entrance, you can finish the game right away.
You main base will be a huge military space cruiser not too far away from the alien planet. The Star Cruiser is called the Blood Avenger. Got the name from my buddy who is a christian, he was telling me in the end of thew world, his god will come and avenge the blood of the saints. Cool religion.