Deus Ex 8th Mission: Brooklyn Naval Shipyards and Lower East Side Cemetery

The 8th mission in Deus Ex takes place at the Brooklyn Naval Shipyards and Lower East Side Cemetery. In this, JC Denton has arrived from Hell's Kitchen via Jock's helicopter with the aim of scuttling the freighter PRCS Wall Cloud carrying shipment of the Gray Death virus.

Augmentation canisters

 * Brooklyn Naval Shipyards
 * Aqualung / Environmental Resistance – In a safe in the base commander's office.
 * Naval Assembly Building and Ship
 * Augmentation upgrade canister – In the the crew quarters, in a locked safe in the laboratory. The laboratory is to the left of the armory.
 * Ship Lower Decks
 * Cloak / Radar Transparency (appearance #2) – In the observation deck (on sub-deck level 2), in a closet locked by a keypad (code 9999)
 * Ship Lower Decks
 * Augmentation upgrade canister – In the safe hidden behind the "Dowd" plaque in the crypt

Weapon modifications

 * Brooklyn Naval Shipyards
 * Range – Inside a crate in the semi-trailer parked outside of the east warehouse
 * Reload – In the base commander building, inside the left cabinet of the desk in the commander's office
 * Naval Assembly Building and Ship
 * Silencer – In the electronics lab of the freighter
 * Accuracy – In the electronics lab of the freighter
 * Laser – Under a desk in the commander center of the freighter

Shipyard
Use the grate at the starting area to reach the first barracks. Up ahead is a patrolling soldier. If you received Vinny's support in the previous mission, the soldier will give you the NanoKey to the main gate.

The area ahead has the following features: While you may proceed through the main gate using the given NanoKey, you may earn a bit more skill points by entering the compound through the sewers. There are many optional skill points in this area. An example sequence of actions that obtains all bonus skill points in the initial area is described below: There are multiple ways to enter the naval assembly building, which houses the freighter:
 * The east warehouse is straight ahead from the main gate. Outside of this warehouse, there is locked semi-trailer with a range modification inside.
 * The ammo warehouse is west of the east warehouse. This building is part of a secondary objective and is labeled with the sign "ammunition storage."
 * The base commander building is southeast of the ammo warehouse (and northeast of the main gate).
 * Across from the base commander building is another building with a repair bot inside.
 * Sewers
 * Enter the sewers through a manhole near the first barracks building. Pass through the chasm with three red pipes (40 SP) and then through the two laser traps (20 SP) that release mini arcbots.
 * While in the sewers, skip the first ladder. Use the next ladder to enter the east warehouse, where you will encounter mechanics and soldiers.
 * East warehouse
 * Enter the northwest office. The left cabinet of the desk contains a datacube with a useful login (USFEMA/Security). This login can be used on the security terminal near the vending machines to disable the office cameras. The right cabinet contains the NanoKey to the semi-trailer outside.
 * The warehouse office has a door locked by the keypad (code 2249, which is found in the base commander's office). Unlock the door (20 SP) and enter the room. Due to a scripting oversight, you gain an additional 20 SP by destroying the door after unlocking it. Inside the room is a security terminal along with NanoKeys for the supply closet, commander's office, and the ammo warehouse. One NanoKey is under the desk; the others are in a cabinet. Use the login (USFEMA/Security) at the security terminal to disable the bots (by putting them on standby). While still logged in, switch to the security options (bottom-left corner button) to open the main sewer grate.
 * Proceed up the stairs above the warehouse office to find a locked door to the ammo warehouse. Open the door using your NanoKey (30 SP) and enter the ammo warehouse.
 * Ammo warehouse
 * In the ammo warehouse, enter the control control room and unlock the three storage units using their respective buttons. Enter storage unit 3 (the one guarded by two bots) to complete the secondary objective and earn 50 SP. Then, climb on top of the raised roof of storage unit 3 to get an additional 50 SP.
 * Base commander building 
 * Exit the south entrance of the ammo warehouse and enter the base commander building. Once inside, use the NanoKey to unlock the commander's office (20 SP). A desk cabinet carries a reload modification. The safe holds another instance of the aqualung / environmental resistance canister.
 * The building to the west of the base commander has a keypad (8675309) which opens the nearby gate. Pass through the gate to obtain 40 SP. From here, the naval assembly building is the to north.
 * Sewer route – The sewers path is optimal in terms of accumulating bonus skill points without having to backtrack. If you opened the main sewer grate at the security terminal in the east warehouse, you will be free to pass through to the next map segment. Note that you won't see the grate if it was opened; however, you will encounter a LAM on the wall close to where the grate was. Once you pass the map transition, you will arrive at the wharf guarded by MJ12 troopers.
 * Ground level entrance – The main entrance is up the stairs near the elevator. The entrance door is unlocked by keypad code 0909.
 * Elevator route – Yet another is to take the elevator upward. Then, enter the control tower to lower the crane. Cross to the other side via the lowered crane and break open a vent opening. Eventually, you'll enter the naval assembly building through a room with a large fan. Like the sewer route, the elevator route also coincides with bonus skill points. However, if you take the sewer route instead, you will may pass through the elevator route (in the opposite direction) at the end of the mission to pick up the skill points along with the elevator route.

Naval assembly building
If you obtained Vinny's support in the previous mission, the soldier inside the security office will be friendly (rather than hostile). However, the MJ12 troopers on the boardwalk near the freighter will be hostile.

It is noted that there are several miscellaneous skill point bonuses in this map segment that do not coincide with the shortest path for purposes of mission completion. Please see the list at the top of this page for details.

If you arrived via the sewers, the security office is accessible from the center of the wharf. In the security office, a DataCube on reveals the ramp access code 6655. If you received Vinny's support, this code can also be obtained from a mechanic in the lunch room. The ramp access keypad is directly outside the hallway from the lunch room. Enter the code to raise the ramp.

Enter the crew are is located on the western deck of the ship. This area includes an armory, an electronics lab (containing a repair bot and weapon modifications), and a sickbay (containing a medbot). To the left of the armory is a laboratory containing an Ambrosia vial and a safe with an augmentation upgrade canister inside. Recall that in the previous mission, JC had promised to find medicine for Dowd, who had contracted the plague. The conversation with Dowd initiated the secondary objective "Bring Stanton Dowd some Ambrosia to counteract the Gray Death." While this objective is not explicitly carried over into this mission, you will nonetheless be able to give the vial to Dowd later on.

The laboratory leads to the third floor, which includes the bridge, the command center (containing a laser modification), and the captain's quarters (code 65678, found in the command center). The objective here is to find the NanoKey that opens the door to the below decks. This NanoKey can be found in the sickbay and the captain's quarters. Once you have the NanoKey, head to the below decks.

During this mission, you will period receive infolink calls from Daedalus. When you arrive in the naval assembly building, Daedalus will tell you that Dowd will eventually send you to Paris to contact his Illuminati associate Morgan Everett in Paris. After enter the lower decks, Daedalus will you inform that you Everett can be reached through Nicolette DuClare.

Below Decks
The lower decks include four main regions: the east room (right side of the map), the bilge pump room, the electrical room, and the helicopter bay (the west room; left side of the map). Also note that there are two levels, and upper level and a lower level, each with a separate hallway.

You begin near the east room, a large room with lots of mechanical equipment. This area has the first two tri-hull weld points. Destroy the tri-hull welds using an explosive (such as a rocket or LAM). Next, enter the hallway and turn left to find a mechanic outside of an electricity-filled room. Talking to the mechanic gives you another secondary goal of shutting down the electricity. To do so, enter the electrical room while hugging along the right-hand wall to find the first control panel (40% strength), guarded by a mini-arcbot. Bypass the panel using a multitool. Then, enter the floor vent nearby to find two more control panels below the floor. The first control panel merely disables the laser-activated trap. The second control panel (40% strength) is the one that you need to bypass.
 * The first tri-hull weld (the one near the north boiler) is out in the open.
 * The second tri-hull weld at the oil reservoir is in an area enclosed by a tall fence. One option is to simply toss a LAM over the fence. Alternatively, to enter this area, use the code 9753 under the bridge to lower the bridge to the control tower. Enter the control tower (gaining 40 SP in the process) and look for a room with a breakable window and a crate. Break the window and travel along the red to enter the area with the tri-hull weld.

Once you've bypassed the control panel, the electricity should disappear, allowing you to destroy the third tri-hull weld. In this area, there's a ladder to the walkway above which leads to the lock door to the helicopter ops room. The door to the helicopter ops room can be opened by the code 64788.

Next, proceed to the helicopter bay to find the fourth tri-hull weld. The four remaining skill point bonuses in this map second are also near this area. Two skill point bonuses are in the helicopter bay (on the helipad, and in the vent below the floor of the helicopter bay). Two additional skill point bonuses are obtained at the cooling systems room accessible via the corridor to the east of the helicopter bay.

The final tri-hull weld is in the area in the map labeled "bilge pumps." Optionally, there is a platform on the upper level to the SE that will give bonus skill points (80 SP). Once you've destroyed all the tri-hull welds, the next step is to turn on the bilge pump by activating the button near the computer and logging into the computer (kzhao/captain). You'll then receive an infolink call from Tong telling you that the ship will tear itself apart. Exit the lower ship and return to the naval assembly building.

Return to Jock on the roof
The next objective is to get to the outside roof of the naval assembly building, where jock has landed. On option is to pass through the AC system. To do so, go to the west end of the wharf, where you'll find an elevator to the crane (if you haven't done so, you may ride the elevator up to the top for bonus skill points). To the right of the crane is a ladder. Climb up to the top and turn right. You will pass through a tunnel, and reach the ventilation fan. Note that there is a skill point bonus behind the grate behind the ladder.

The ventilation fan is destructible. Destroying it allows you to climb the ladder to the roof safely. Proceed to the roof and find Jock's helicopter. Tracer Tong will tell you that Dowd has discovered who engineered the virus. Jock will fly you to the cemetery to meet Dowd.

Lower East Side Cemetery
The gates are locked, but the gate keeper will open it for you. Once inside, proceed to the crypt and speak to Dowd. Dowd will confirm that the next objective is to track down his Illuminati associate Morgan Everett. Dowd will also inform you that the Gray Death virus has Everett's signature, as well as that of Bob Page. If you found the Ambrosia vial on the freighter, JC will give it to Dowd. However, even whether or not you retrieved the Ambrosia has no effect on the story. Inside the crypt, note that the "Dowd" plaque on the wall hides a locked safe containing an augmentation upgrade canister.

While speaking to Dowd, it becomes apparent that the gate keeper was an MJ12 operative (if you kill the gate keeper before speaking with Dowd, Dowd will provide a humorous response: "Starting to think like us, huh? Be careful. Paranoia's a drug; you can get addicted."). Sure enough, MJ12 is already prepared to ambush you on the outside.

Jock is unable to land due to an EM disruption field. In the gatehouse, find a keypad (1234) hidden behind a wall painting. Then, destroy the EM field generator to complete the objective. Jock will land his helicopter and will take you to Paris.