After Nate opened the gate that blocked access to the rest of the flooded city, he and Elena continued onwards, searching for a way into the customs house. After reaching another drop-off point, Nate hopped off and ventured through the city, searching for a way into the tower. Elena took the jet ski and told Nate they would reunite at the customs house once he managed to gain entry.
After fighting several groups of pirates, Nate finally made his way to the top of the tower. Using a cable as a makeshift zip-line, he slid down into the building, through a large hole in its roof. Once inside, he opened the door for Elena, then the two continued through the customs house.
This chapter is a continuation of the previous one, as you are still in control of the jet ski. The same rules apply—kill the pirates and shoot the barrels that stand in your way. Continue to follow the linear path until you reach a gate, at which point you will need to shoot the chains on either side to lower it. Once you are inside and you dock the jet ski, Elena will leave, leaving you to explore on your own. Two normal pirates and one wielding a Moss-12 will ambush you, but they are all easy to take down. You can also find two Mk-NDI grenades lying around before you press on to the next area.
To reach the area, you will need to swim through a narrow path of water. You will be attacked head-on while doing this, so you should make it to the other side quickly and take cover immediately. You can grab the ledge at the end and hang off of it to pick off any nearby enemies before pulling yourself up and over to combat them. You can find another pair of grenades on top of a crate in the lower-left corner as well. Once you take out this group, climb a small set of stairs, after which you can jump onto a nearby balcony platform, and then on top of a broken wall. From here, jump to the next wall and pillars until you reach the top of the locked gate, at which point you can simply drop down and immediately engage the next set of enemy combatants.
You should immediately take cover, as a pirate wielding a Moss-12 and another wielding a Wes-44 will ambush you from close range. Be careful upon going through the first opening on the right, as a pirate with an M79 will be ready to shoot you right away. Take care of him and any other nearby pirates, then deal with the group entrenched in front of the tower. The M79 will be useful here, but simply hanging onto the buildings and using them as cover is a good strategy as well. This allows you to save the grenade launcher for the final group that emerges from the tower all at once.
Once you have killed them all, you can continue to the open tower entrance and head inside. There are a couple of remaining pirates in here, who can easily be dispatched with melee attacks if preferred. Once cleared, you can use a nearby lever to move a chain, which you must then climb to reach the second floor. Here, climb a series of white-marked handholds to reach another lever, followed by using the same handholds and a pair of tiny platforms to make your way around the room to reach the second chain. At the top, a single pirate will ambush you, but he is otherwise easy to take down. Afterwards, go around until you reach the stairs. Climb them to get to the top, and you will see an opening at the edge. Press and you will descend the wire to reach the customs house. After this, you will hear Elena's voice, telling you to let her in.
Approach the door downstairs and shoot its lock off, then press to open it. Note that taking too long to open the door will lead to Elena being shot down. Once the two reunite, the next chapter begins from here.