I make this so somebody can come up with ideas! I'm not creative enough, so someone else can build off of this!
A simple idea I am kinda surprised they have not done yet in the mainline games is corporate badies that want to get rid of natural environments to build things like factories. Since our region is based on the Great Lakes area in north america, perhaps they want to drain one of the lakes to put in a city of some kind, the player stops them and helps build a floating town instead that lives in harmony with the lake instead of destroying it.