When you take control, equip the Mk2 and crawl to the eastern side of the
ship, which is the left in this case since you're facing south. Crawl down
the path here and shoot the two Haven Troopers that begin walking towards
you. If you can, aim for the one behind the other to avoid her partner from
getting suspicious. Once they've both been knocked out, continue down the
side of the ship. Another pair of Haven Troopers jump down from the second
floor in front of you, so take them out as well.
Keep heading down this path until you reach the two Haven Troopers' bodies.
Another Trooper will begin walking in Snake's direction, and they may become
suspicious if they see the bodies lying around. Quickly knock her out with a
headshot, and wait here for a moment. Two more Troopers are patrolling this
area, but you can wait for them to walk away and sneak by. As you approach
your last victim's body, another Haven Trooper be show up farther down -
knock her out, too.
Here's where the trouble can begin if you slip up. A Gekko is roaming around
the south end of the bow - directly in front of the porthole you need to
enter. We can worry about that later, however, as the task at the moment is
to simply reach the exit first. There are some crates and a large cylindrical
tank labeled "R1" in front of you, so stand up and hug the tank to squeeze
between them and avoid entering the main area where the Gekko is. Once on the
other side, begin crawling south again, but keep an eye on your radar for any
hostile blips. Two more Haven Troopers will jump down from the second floor,
so keep your Mk2 on hand and take them out.
From here it's a straight run to the exit, but there's a catch. The door you
need to go through is airtight, and you have to turn the handle several times
before it opens. This can create problems if you've set off an alert, as you
probably won't have the time to open it before being attacked.
With this in mind, crawl around the corner and hide behind a crate east of
the door. A second Gekko will jump down directly in front of the door, but
Mei Ling comes through when it counts, and one of her ship's canons hits the
Gekko, destroying it. With that out of the way, wait for the remaining Gekko
to walk away, and then quickly run over and open the door. Once inside, grab
all of the items and enter the elevator.