This is the final mission of the game, and it can be as tough or easy as you make it. Luckily, there is a very easy way to finish this mission without too much trouble. When Samuel drops you off, he'll talking to you a little and comment how you went around and didn't cause too much chaos, then he'll drive off. There are two ways to get inside of the fort; the beach side entrance, and the harbor side entrance.
When he drops you off, look to your right and you'll see two large rocks with cables attached to them. You'll want to swim to the one farther away from you and get on it. Jump onto the cable and walk along it all the way to the fort. When you get to the end, Blink on top of the guard tower there.
TO THE LIGHTHOUSE
Once you're on top of the guard tower, head left and onto the pipes, following them to the next guard tower. Keep going in the same direction, getting on the top of the wall and Blinking to the roof of the structure at the end of the wall. From the end of the roof you're on, you can see a small ledge on your left, which is where you want to end up.
On this ledge, hop on the railing and look up towards the building. You should save before the next part, as it can be a little bit of trial and error. You need to Blink to the top of the building you're looking at, but it can be a little tricky to get the right spot. Once you get on top, Blink to the cable on the right side of the bridge.
Follow this cable all the way to the lighthouse, keeping an eye out for a guard that may be on the stairs. If the guard is at the bottom of the stairs, you're good. At the end of the cable, Blink on to the top of the elevator and drop down through the hatch. There might be a guard at the top of the stairs right next to the elevator, but he will have his back turned. Once you're inside, use it to get to the next area.
EMILY AND HAVELOCK
When the elevator stops, you'll be at the final area of the game. Get out and then Blink to get on top of the elevator. Use Blink to get onto the beams and then onto the top of the structure. Once you're on top, get onto the glass roof using the nearby air conditioners.
Once you're on this glass roof, head to the far side where the stairs are located. Get on the stairs and go down until you get to a glass door. Go through the doors and read Havelock's journal on the desk to fulfill the optional objective if you want. This is the room where Havelock is keeping Emily, but he is also here, as well as Pendleton and Martin, who just happen to be dead. Sneak behind Havelock, knock him out, take his key from the table and free Emily. You have just completed the game, so enjoy the Low Chaos Ending.


