Hmm, I think we could use Renz's idea with a few tweaks.
There would be natives and settlers. Pretty much opposites. Natives want the region covered in nature, while the settlers want to bring technology and inventions.
At first, the protagonist sides with the settlers, and the natives are the "evil" team. Then, the settlers, with the help of the player, slowly start to take over. It turns out, the natives were the good guys and the settlers had an evil plan! From this point on, the protagonist joins the natives to stop the settlers, once and for all...
I dunno, I just wrote whatever came to mind :v