They'll begin by scrapping the settlement, decide for themselves where zoned plots should be placed, and then set about building along with the other NPC settlers you've recruited.
You can assign a city leader for each settlement, choosing from Fallout 4's NPCs companions, and put them in charge, as if making them mayor. Rise of the Commonwealth, the expansion to Sim Settlements, takes the idea a step further by letting NPCs not just build their own stuff but actually plan the settlement completely without your input.
