Covenant is a small settlement along an eastern section of the river headed towards the ocean. The people of the town seem slightly off… a too good to be true scenario. Honest Dan, there investigating the disappearance of a caravan, and the caravan owner’s daughter, knows that something is wrong, and he enlists you to help investigate.
A little snooping leads to an underground base just across the river. There a mis-guided scientist is conducting “research”. Negotations go bad.
NOTE: This will make the settlement of Covenant aggro against you. They attack on site. Once you’ve killed them Covenant becomes a new settlement for you to manage, and you’ll have to bring in new settlers. I assume allowing their experiments will do the same