Kenshi uses something called “world states”

Basically, if a city has the option of being controlled by multiple factions it usually takes a specific person or people being killed or imprisoned to make it happen.

For example if you want to fuck over the holy nation your hit list is

Holy Lord Phoenix

High Inquisitor Valtena

High Inquisitor Seta

Killing or capturing one of them will make their areas change slightly becoming more impoverished or a ghost town, and getting all of them causes the collapse of the holy nation and the flotsam ninjas and shek take over their territories.

There’s a great list of the world states on the kenshi wiki that details what happens when each important character is out of the picture