With no usual means of entry, Nate began scaling the outer walls of the fortress. Once inside, he found himself face to face with several groups of Eddy Raja's pirates. After clearing out the forces in the first major courtyard, Nate continued searching for Elena, heading toward the tower ruins where she had originally landed and left her parachute.
Upon reaching the tower, he found the parachute harness empty and still no sight of Elena. He climbed up to a zipline, from which he ziplined down into a small watchtower. There, he spotted Elena in the upper windows of the fort filming the scenery. He then took a look down at a locked gate below and spotted a pirate. Using the pirates' language, Nate contacted the gatekeeper via the radio on the table to get him to unlock the gate. Unfortunately, the guard suspected something and opened the gate only to bring in reinforcements, much to Nate's dismay. Once again, Nate found himself in another firefight with another wave of pirates in the same place as before. Following this gunfight, he proceeded into the flooded chambers of the fortress, looking for a way up to Elena's position.
Climbing the walls
There are several small ledges, some of which will crumble and cause you to fall, and a couple of vines along the wall of the fortress. When swinging on the vines, you must build up enough momentum before swinging your way further. Eventually, you will be able to make it inside Once inside, head right into the hallway and turn right again to find another open window. After climbing out, climb around the wall again until you reach another window. Grab the nearby vine and press to have Nate bust through the window.
Once you are back inside, you can find a Micro - 9mm on a nearby crate, along with a few Mk-NDI grenades. Head through the hall to the right, then turn left to enter an area where you will encounter some enemies. Take out the enemies on the ground level, but beware of the ones hiding out on the walls above you, eventually taking those out as well. Head towards the end of the wall and carefully jump down into the yard below. Head up to stairs leading into another courtyard, where you will be immediately spotted by a bunch of pirates. Take out a few of them before they get to cover, using the explosive barrels to your advantage.
You will not be able to charge ahead due to a pirate manning a mounted machine gun on the left side, forcing you to either throw a grenade or flank him by using the crates and truck for cover. Once the area is clear, you must now search for the tower Elena's parachute is in. Head to where the turret is to find a doorway, leading into a room where a shotgun pirate attacks. After defeating him, head to where he came out to find some stairs that will get you back on top of the fortress wall. From here, you will be able to make your way over to the tower.
Once there, climb the stairs within it, and when prompted, press to trigger a cutscene that leads you into the watchtower. You will then be fighting another wave of enemies. On the table is a Wes - 44, a powerful revolver, but save its ammo and use something else to blow open the lock on the door. Use your superior position atop the walls to your advantage, and after clearing out the enemies, head inside the building.
The flooded chambers
You will drop into a large flooded hall. At the right end is another mounted machine gun, so quickly drop down from the platform you are standing on and use nearby sections of the wall for cover, only moving while the pirate is forced to reload. Halfway through, you need to sneak into the room on the right, occupied by a lone pirate, and be able to grab an M79 and several grenades. Use either to attack the pirate and blow up the turret. Once done, head down to the end of the hall and enter into another larger chamber. Three pirates will ambush you here, two of which have a height advantage on you. Do not venture too far out into the room, as this will trigger a second wave coming through windows on the left side, and note that after clearing them out, a third wave will come through windows on the right. Finally, after those have been cleared, a pair of pirates wielding the Moss - 12 shotguns drop down from where you entered.
Once cleared use some nearby rubble to reach the mounted platforms on a pillar, from where you can jump to the exit passage. This room requires you to raise the water twice, by using handholds on the walls to climb to two winches, both of which allow you to flood the room even further. First head for the left winch, and then the right, after which you can climb out of the water and continue deeper into the fortress.