After the fence comes down, follow your squad through it. In fact, just keep following them for a while and the only thing you will have to watch out for are the mines. Despite being big and red, they can still be hard to see so pay close attention to your sonar which will beep in the direction that they are. Keep following your squad and head down until the sub passes by. Once it's by you, come up behind it and plant a bomb at the spot marked on the tail.
Once you've surfaced, head up the tail end of the sub but watch for the two enemies that are going to peak over. Kill them and make your way up to the topside of the sub and you'll see three more enemies at the far end of the sub. Get rid of them and someone will drop a frag in the hatch then proceed down into the sub. At the bottom of the sub, follow Sandman through a door. In the next room, kill the two men escaping through the door and then follow where they were going.
Go down the stairs and through the hallway. Kill the few men here and watch for fire from the right. Wrap around with the hallway to the right and kill the two men at the end. Proceed toward where they were and the door ahead of you will open with two more enemies behind it. Kill both. Go through the door they opened, take a right and a quick left up the stairs. You'll enter the engine room and have to deal with enemies all around. There are plenty of places to take cover but head all the way to the left so you are under the catwalk and try to take out as many enemies as you can, including up above you. Thankfully you won't have to guess where they are because all of your enemies will have laser sights which you can trace back to their source. Once the room is clear, head through the door at the back of the bottom floor.
The next room will be much the same but with more enemies on your floor. Kill them all but be careful as you move forward because it's very easy to let one slip by you. After, go up the stairs at the back right and walk up to the door to breach. If you've never breached before, the door will blow open and you will enter a slow motion state where every shot is an instant kill. In this case, kill the man charging you slightly to the left, and then just start from the right and work your way left. There are five enemies in all. Don't worry if you don't get them all but don't be surprised if you do. Head to the back left of the room and you'll have to use a console to launch the missiles. Turnaround and head out through the ladder that Sandman climbs.
Once you are outside and on the boat, you'll have to follow a relatively strait forward path. After a short sightseeing trip, you'll be attacked bay boat on the left. Don't aim for the enemies. Aim for the giant red mines on the back end of the boat by the turret to destroy the boat. After that, you just have to follow the lead boat until you get to the point where the chopper drops down into the water. Head right up into the belly of the chopper.
