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You've just entered the sublevel decks of the ship, and are about to place 5 explosives in key points along the hull, indicated by X's on the map. I'll provide you with an easy to follow guide, though it doesn't matter which order you do any of the steps in, even reversing the bilge. Once down the stairs, you'll be on an upper level catwalk in the engine room, with stairs down on either side of you. Take the left stairs and head to #1 on the map. This tri-hull weld point is beyond the square walled-in area so you'll have to toss a LAM over the wall. However, there are grates down there so if you have the speed aug, and can move a crate to the right side, jump on and over the wall, you can score some bonus supplies before the explosion. There are climbable metal crates once within.
As soon as you hear the explosion, you'll score 120 bonus skill points and a couple guards will likely come searching the area. There's a semi-safe area between the #1 and #2 points on the map if you crouch under the giant turbine. After the guards move out or are taken care of, hit #2 with another LAM for another 120 skill points. Head to #3 where a keypad rests on the pillar near a ladder. Type in the code you got back upstairs in the sick bay, 9753, and climb the ladder to the bridge that moved into position. Cross it for some more bonus points.
In the room beyond and up a ladder are three sailors. Just above the ladder is a security computer terminal so you can use it if you're patient and their backs are turned. Use the login "root" and "reindeerflotilla" to disable all the cameras and open a door below.
Exit the way you came, down the ladder and through either door at the bottom which leads to the area near #5. Beware of guards, both inside the room between areas, and patrolling the long hallways of #5. Enter the hall and head right toward #6 and the Bilge pump area. There are a couple sailors inside so be prepared. At the bottom, flip on the bilge pump using the switch and logon to the computer using "root" and "reindeerflotilla", and reverse the flow. Toss a LAM near the weld point in the room, and head back up the stairs and the other direction toward #7, electrical.
Before the door you'll find an electrician and repair bot. Take the nanokey behind him on the crate, which opens the door on the second floor of electrical, just beyond the bridge.
Here's a little secret. If you were to turn right at the electrician and go into the cooling system room in the center, climb the ladder, float up to the hole opposite the security camera, and crawl through it, you'll eventually find some crates and supplies including a cloak/radar AUGMENTATION CANISTER
and GEP gun. It eventually exits in the Bilge room, opposite where you entered... and these supplies can also be entered from
the Bilge room, so long as you can jump high using speed from one of the pumps. Back to the task.
Enter the Electrical room and beware of a spider around the corner at #7. These buggers are tough unless you happen to have the Spy Drone augmentation, which I forwent. Either use a high-powered gun, or, a simple EMP will do nicely but I like to save mine as they are hard to come by. Since the repair bot is nearby, it's not such a big deal to lose health and use your energy on regen.
Around the corner is an electronic panel that can be bypassed. Do it, and head down the nearby grate. Crawl through the shaft, and before the first laser, bypass the electronic panel there, and once its disable, the one beyond to complete your secondary goal of clearing the electricity. Now you can cross the bridge above. But not before first tossing a LAM on the weld point in this room, so do it, climb the ladder and cross the bridge. Use your nanokey from the electrician's crate outside the room on the door, and use the security computer terminal to the right of the door to disable cameras and/or switch turret AI in the helicopter bay beyond. Deep inside the room at #8 there are sailors. Your only goal is the grate along the wall to the left of them, so I'll leave their handling to you.
Exit the helicopter operations room via the grate on the wall and head down to the lower room just outside the helicopter bay; you can see it on the map. There are guards patrolling the area, as well as a repair bot, and your weld point is on the left wall near #9 as you exit into the bay. Sneak over, toss a LAM and get ready to go because the ship is about to sink. You actually have plenty of time to get out. How much? I'm not certain, but I've never not made it. [ed: it would be really cool if it did actually start to sink and water slowly began filling up, eventually requiring that you swim the last floor.]
The easiest way out is by running straight out that corridor to the right of the helicopter bay on the map, to the cooling systems room, take a right to electrical, then another left at the repair bot, back up the stairs to above decks, hang a right and exit the starboard side (where it says "Enter" on the previous page). Head down to the dock, take a right until you get to the door on the left. Take the ladder back up to the shafts, and back out the way you entered... not having to deal with any spiders or fan because you already disabled/dismantled them on the way here. Just head up, out onto the roof where Jock awaits in his helicopter to take you to the cemetery, a very short level.