Sure, you eradicated all of your enemies at Cottonwood Cove rather easily, but you won't have an easy go at the enemies at The Fort. But if you found violence at Cottonwood Cove, then expect to find a scene ten times worse at The Fort. If you found peace at Cottonwood Cove, then you'll no doubt find peace at The Fort too, so long as you keep your weaponry holstered and go about your business in a quiet manner. What you want to focus on here, whether things turned ugly or not, is getting to the half-destroyed dock working into the water, where you should be given the option to access the Legion's primary fortress in the Mojave Wasteland, a location simply known as The Fort. If you're friendly with them, you'll have no worries about getting through here, but if not, get ready for a bit of a fight! There are enemies not only running around outside, but also within the two buildings here, so you'll want to clear out those buildings (if things turn violent) in order to assure that you don't get flanked or otherwise unexpectedly attacked later on. Upon your arrival at Cottonwood Cove, you'll run into the small contingent of Legion characters that occupy this fortress. Either way, though, the first place you want to head to in order to get this misadventure underway is Cottonwood Cove, which is located at the far southeastern edge of the map, north of Smith Mesa Prospector Camp and Cottonwood Overlook. For what it's worth, we weren't friendly with the Legion at all, so we definitely had our hands full. But if you're friends with them, this will be a lot easier.
If not, expect that you'll have to do battle with droves and droves of Legion personnel, including with their entire leadership. You don't have to necessarily be friends with the Legion to go through with this quest, but it will certainly make your life a lot easier. Thus, you're going to have to have yourself sorted out with the Legion one way or the other. This particular quest will force you into the very heart of Legion territory.