The first thing you need to know is that you are PREACHER for this mission and the gruff looking guy next to you is Mother, who will be calling the shots for the most part. If I tell you to do one thing and he tells you to do something else, you do what he says.
You'll automatically make your way out of the water and gain control standing behind an enemy. If you've never played a shooter before, follow the prompt on screen to shoot the man in the back of the head. He'll slump and you'll grab him to keep his fall quiet. Mother should be up by the base of some stairs. Climb these stairs with him and he'll lead you up to take cover behind a white van.
Just beyond the van is going to be another enemy facing away from you. Sneak up behind him and this time you are going to learn how to do a melee attack. Follow the prompt on screen once again to take him out.
Mother is going to run up ahead and take cover behind a truck that's been turned on. Go up next to him and use the "activate" button to plant the bomb on the back of the truck. Mother will move to the left and take cover behind the guard house. Follow him and when he says to "smoke him", shoot him. Interestingly, if you fail to, Mother will down him instead. I learned this when I was still trying to figure out how to throw a smoke grenade...
Anyway, take out the guard in the guard house and then move across the street to Mother's new cover position. You'll automatically take out the detonator for the explosives you planted. Wait for Mother to give the go ahead and then use the right trigger to set off the explosives.
What was that!?
The plan was clearly to blow up the truck so what's up with the ship? Anyway, get ready to push through because you've got to get out of here. Mother is going to move up along the right side near the boat until he stops by a large red shipping container. Just to the left of this crate will be two enemies approaching.
The next two enemies you encounter will be harmless. After watching two men on fire die on their own, keep a focus on the open shipping crate ahead. An enemy will appear in this crate and then after that, another will appear atop the crates stacked two high on the left.
Go through the previously occupied open crate and out the back of it. This is going to put you on a sort of track created out of shipping crates. Follow mother around this track until it takes you back down to the docks. You'll hit the bottom of a ramp made of shipping containers and on the right will be a the water and a few walkways scattered above it. You'll find two enemies on this walkway so make sure you turn right as soon as you hit the bottom.
After taking them out, Mother is going to lead you under the docks to another walkway. Along the way, you're going to pick up a helicopter as a tail. Thankfully, you're also going to find a SMAW on this walkway so grab that and use it to take out the chopper. You may want to lead a little bit but you should still have your crosshairs over the chopper. One good shot will take that chopper out, no problem.
