My idea is to take the EPA from fallout restoration project and fill it with respawning hostile supermutants that increase in strength the deeper you get into the base, the bottom floor will only be reachable by a well organized group of players. On the bottom floor there will be a boss character that has in its possession a GECK. This geck when brought to the faction base and has science skill used on it will change your faction base, adding trees and fruit/fibre plants. For the cave base it would only affect the outer area, making it look like the wooded cave entrance with some random plants scattered about(Possibly a semi dense forest). The gas station would get a similar treatment and the farm could get some other bonus since it already has these benefits, possibly respawning trees that can be cut.
The top level of the EPA will have tough nightkin with laser rifles, once they are killed the players will have to get through the basement floor by floor, the top ones filled with a mix of supermutants and centaurs and the lower having robots, culminating with a boss battle with a sentry bot.