Nate is ambushed by a large group of Eddy's pirates inside the large domed building. After fighting his way through them, he advances to the motorboat that will get him and Elena off the island. When he reaches the harbor, he spots some pirates about to make off with the boat. He is then surprised by Elena who has made her own way to the boat. As Nate prepares to take out the pirates, Elena stops him and shows him video footage of Roman escorting the supposedly dead Victor Sullivan onto a helicopter with Navarro. As Elena begins to question how much Nate trusts Sully, pointing out that Roman and Navarro are not exactly holding him at gunpoint. Nate tells her that Sully is not a backstabber, and takes out his map to figure out where they were headed. Following Elena's direction, he works out that they were traveling north, towards the monastery. The pirates have driven off in the boat, leaving the two with no other option but to travel after Sully.
They advance further through the drowned city, passing over a rope bridge that spans an enormous gap between two buildings. Nate points out scorch marks on the edges of the buildings, explaining that they were packed full of enough gunpowder to blow them wide open. As they cross the bridge, one of the planks beneath Elena gives way and she falls. Nate grabs her arm, but is unable to pull her up until she drops her camera into the water far below, which disappoints Elena. The two continue to press on and eventually arrive at the city's outer limit, on the bank of a river, where a jet ski has been moored.
When you first enter the room, don't go completely down the stairs. Instead, jump down over the railing ahead and you will spot a Dragon Sniper rifle right there. Grab it and focus onto the pirate on the machine gun. Then snipe the guy on the high walkway on the right, then use whatever ammo's left on any other enemies. Then take cover at the barrier ahead and grab the M4. It has small ammo, but is highly effective against the pirates, so keep it with you throughout this chapter.
After taking out the pirates, head up the stairs to the turret. More pirates will come in and shoot at you. Smoke them with the turret, then head up the stairs to activate the winch to the door. Quickly head back down and pass through the door before it shuts. The drop down and head down the stairs to trigger the following cutscene.
After the cutscene, head up the stairs ahead and prepare for some more shooting. Watch out for the guy with the grenade launcher, who happens to corner you upon coming up the stairs. Clip the other two guys and then head up the stairs on the left side. You will then approach a wooden bridge. Cross it to trigger another cutscene. After that, turn left and pass a couple set of stairs. Drop down and head up the path leading into a small room. Stealth attack the pirate, then take out the others on the stairs. Head up the stairs and you will approach the river bank with several more pirates waiting for you. Once you take them all out, the next chapter will begin.