Here's a quick backstory. The waitress who shot Valentin turns out to be Xenia Onatopps. Again, she doesn't look like Famke Jannsen whom you've seen in the 1995 movie and N64 version. It's no secret that Xenia and supposedly another guy is coming to steal another EMP Helicopter so you're sent to Dubai to put a satellite track on it. What's probably worth mentioning the most unlike the N64 version that shows her in the train and in the jungle, here, you get introduced so you know what she looks like. It's important you know who she is before the final confrontation. If she's not there at the start, simply there's no logistical reason why she's in the jungle attacking you.
The Short Lived Sergeant Briggs
After a short scene with a guard. Go to the stairs where you go to meet him. Unfortunately he gets shot by Xenia. Like the Airfield, at least for the first half, stealth is out of the equation. After the first confrontation, as soon as you get to the area with the right hallway, go through the rightside where you can take control of the turret gun via cellphone. Take care of the remaining guards and open the metal door via cellphone.
Ship Shootout
Go through either hallway and shoot yourway to where the ship is. At that point once you enter the ship, your allowed to use stealth as an alternative. Sneak or shoot your way through the ship to where the lockdown is. Also look out for turret guns that you can control. So if the phone icon is there, hack it so it won't permanently kill you. From that point, its better to take care of the guards first than use your phone to take down to areas: down where the big engine is and on the left area where the computer area is.
Helicopter Tracking Device
The final area is the cargo area that will take you to the top. First, shoot or stealth, then go to the final area beyond the two cars to release the final lockdown. Yet again, stealth is thrown out the window. So shoot your way to where the two cars are standing. Shoot again as you go up and you have a chance to use a phone as a tracker before you drop down.
The Ship Escape
Just when you think it's over, two guards come out. Shoot them and get ready to escape. You go through one hallway, as the second hallway is open. Also the danger is the helicopter got missiles. So wait until the missile already blow the left side so you can get across. The third hallway, go up the stairs to another open hallway. Get passed as soon as the missile blows the left side. The fifth area has one guard try to shoot you down the stairs. As if the guard cares about his own life! Anyway go up the stairs to the exit but that ends the sequence that after a second missile, you jump into the sea in a final cutscene. There goes the helicopter.
Agent
As you enter the ship, you got three hostages to save. The catch is that each place has a breach. As soon as the slow motion kicks in, shoot the guards to save the hostages. The later two has red barrels so resist shooting that as it will let you fail the mission. Lastly, use the silence pistol. You can shoot the barrels in Operative difficulty but not in Agent difficulty in which the hostages are more important than you.