Deus Ex/New York City Dockyard

You are dropped in a lot next to the naval base. From here, you can safely visit the front gate with the two soldiers and speak with them. If you spoke with Vinny in the Underworld tavern, they will give you a few keys and let you know that the guard at the main building will let you pass. Otherwise, you will have to find another way through, either by killing the soldiers to using the underground tunnel.

Underground tunnel
The first obstacle in the underground tunnels is a gap. To get past this, leap from pipe to pipe.

The second is a set of blue beams that will release small spiderbots when tripped. You can either disrupt them with an EMP grenade, or use a multitool on the nearby electrical panel (in the lowered section) to disable the center beams, allowing a low crouch-jump over them.

The first ladder bring you inside an alley within the main base; A soldier is patrolling the alley, and there are two military bots patrolling the area outside of the alley.

Continue onward to find an open area; there is a LAW launcher here. To disarm the lasers, you need to pick the lock to the grating before them, and use a multtool on the panels. You can opt to use the ladders here to enter the warehouses just before the main compound. You can also enter the compound past the lower grading. To open it, you have to surface at the farthest ladder (avoiding two military robots), pick the lock to the closet, and turn the valve. The gate will open, and you can use the sewers to head directly into the water that leads to the superfreighter.

Outer naval base
If you choose to take the main entrance, there are several routes you can take. You can go through the east or west warehouses, explore Walton Simmons office building to the left, or head all the way west to get a route to the crane and main entrance.

East warehouse
The security office at the east warhouse is protected by the code 2249. Misentering the code triggers the alarm.

West warehouse
The west warehouse contains two security bots. If you enter by the front, quickly run to the office in the left corner and configure them to your advantage. If you entered by the east wareshouse, run quickly to the north and avoid the robots.

Simmons office
The building just left of the main entrance is Simmons office. It contains a regular augmentation canister, and also codes to some locations within the base.

Wastern building
If you head all the way west, you get a building that allows you to enter the main compound, bypassing most resistance. There are blue beams beside the building, which release a military robot. Inside, you can use a repair bot to recover bioenergy, and use multitools on the keypad to open a safer path.

Entranace
The main entrance to the compoind requires the code 0909. If you don't have the code, ride the elevator to the top and break open a vent for an alternate passage (filled with mini-spiderbots) or turn the valve and approach via the sewers. These alternate routes provide some skill points.

Dockyard
By speaking with the mechanics or through a few other sources, you can obtain the code 6655 to raise the access ramp. However, you can also swim to the other side of the ship to climb, extend the crane and climb across, or simply jump onto the freighter from the elevator (which isn't recommended, but can work.)

Superfreighter
You should already have images for the superfreighter, as given by Dowd.

The captain's quarters can be opened with the code 65678, as found in the nearby control room. You can get credits here, as well as information about the captain himself and the code to the armory, 71324. You may also collect around 2250 credits as well.

Sickbay contains the code for the engineering room, 9753. Check the desk within this room for the key allowing access below decks.

The code for the command center and operations is 83353, and can be found in electronics. Electronics also has a repair bot.

To get ambrosia for Dowd, check the central table of the Chem lab.

Below decks
To enter the subdecks, you need to have the key from the desk in sickbay. You can't destroy or pick the lock for the door.

In this location, you need to destroy five tri-weld points with explosives, then reverse the bilge pumps.


 * 1) The first is in the front of the ship, ont eh right corner.
 * 2) The second is in the front of the ship, behind two obstacles.  You can see it if you jump over the barrier, and you can destroy it by throwing a grenade into the general area.
 * 3) One is located at the front left of the ship.  An electrician will mention that there is electricity sparking about in the room.
 * 4) One is in the hangar.
 * 5) One is in the bilge pump room.

Once the tri-weld points are destroyed, head to the bilge pump room, turn on the pumps, and use the computer to reverse the flow.

Exit the ship, and head to the outer naval base, and meet Jock on the roof near the crane.

Graveyard
Jock will drop you at the graveyard. Press the callbutton to be let in.

Head into the mausoleum and speak with Dowd. When you leave, MJ12 have arrived as part of an ambush, and have a generator that prevents Jock from landing. Once the generator is destroyed, you can enter the helicopter to complete the mission.