Casualties of War
This becomes available immediately after killing Jacob in Only You.
Head to Jacob's Armory near McKinley Dam, southwest of St. Francis'.
There are only four guards outside, but they tend to be in sniper towers or by mounted guns, so it's good to take them out from a distance.
When the lot is clear, mosey on in. Your companions, of course, will will wait outside, because why would you want help assaulting an enemy bunker?
Arrows and throwing knives are good for this first section- enemies are patrolling aimlessly, and not expecting a fight. Take them out one by one.
There is a heavy stationed in front of the Mess Hall entrance. This corridor has entrances on the east and west- go to the west end and come up behind him for a takedown.
Follow your marker into the mess hall, and down the stairs.
There's heavy just through the door. Lure him out with a rock for the takedown.
He's the only guard in the room, so just follow your marker through,and down the corridor. You'll pass many medkits and turret guns, but none worth commiting to memory.
You'll pass a locked Storage Room door on your left. Ignore it, and enter the control room on your right, then hit the big red button.
Turn around and enter the now-unlocked Storage Room door.
This is actually the same room you just passed through after ambushing the heavy, but now the south door is open- snipe the hostile there.
There are two other hostiles in this section, including another heavy. Once more you can employ the rock-by-the-doorway trick for a takedown.
Keep following your marker. You won't encounter another hostile until you enter the labs, where a Blissed out VIP doctor is shambling about.
But he's the only baddie here. Take him out, then follow your marker to Pratt's cell. Hitting the yellow door switch triggers a cutscene, in which Pratt is happy to see you.
Follow your marker to escape. At no point will anyone use the many, many mounted guns you passed earlier to attack you. In the first room you encounter, there is a flamethrower heavy backed up by 3-4 regular fighters. You can use the stairs here for a dropkill on the heavy.
Exit using the stairs on the south side of the room.
There are two hostiles just past the entrance to the 'Reservoir' section.
In the next room, there's a heavy near the top of the stairs. Rocks can work here, but you might attract unwanted attention from other hostiles. Consider an explosive or LMG instead.
Clear the handful of lesser fighters, then head out through the barracks.
There are actually no more hostiles to fight, just make for the exit door.
Reach a safe distance beyond the parking gate to liberate the region.
Wait through the cutscene is which everyone is very cool about not pointing fingers, then regain control back in the Den, with mission completion.