Here is a list of world states I have discovered. If you discover any yourself, feel free to tell me and I will edit them into this.

Flotsam ninja's:

If Moll has been disposed of, Flotsam village will be occupied by The Holy Nation. The majority of buildings will fall into ruins, while the bar and several others will be occupied by Holy Nation members, making it a decent rest stop.

If Moll is disposed of, Flotsam safehouse will become an ambush site for the Holy Nation.

If Mani is disposed of, the Scout Posts will be claimed by the Holy Nation.

If the suspicious lab is cleared of cannibals, it will become the Flotsam Fortress.

Dust Bandits:

If the Dust King is killed or captured, the Dust Tower will become an outpost for the holy nation.

Black Dragon Ninjas:

If Dimak and Buzzan are defeated, the Tower of Ninja's will fall to the Holy Nation.

Fog Men:

If the Deadhive Overrun is cleared of Fogmen (specifically the "Big Fog Prince" added with this mod) the Holy Nation will reclaim it. They will rebuild the Y-House and make it into a Barracks and rebuild the bar.

If the prince inside of the Tower of Fog is killed or captured then the Western Hive will take over the tower.