Deus Ex 3rd Mission: Brooklyn Bridge Station, Mole Tunnels, and LaGuardia Airport

The third mission in Deus Ex takes place primarily in Brooklyn Bridge Station, Mole Tunnels, and LaGuardia Airport. The beginning of the mission also features second visits to the UNATCO Headquarters and Battery Park.

In this mission, JC Denton must locate the airfield where the NSF has moved the Ambrosia. The mission eventually takes JC to Juan Lebedev's hangar at the LaGuardia Airport where he encounters his brother, Paul Denton, who had recently been fired from UNATCO.

Goals
Goals are listed below based on the location at which they are obtained. * Received after talking to Curly

* * Given by Charlie Fann

*** Given by El Rey

Collectibles

 * UNATCO Headquarters
 * Weapon Modification: Recoil – In the locked cabinet in the conference room on level 2
 * Weapon Modification: Accuracy – Given by Sam Carter
 * Helibase
 * Augmentation Upgrade Canister – In the secret room in the control room, opened by a switch near a plant in the corner
 * Weapon Modification: Range – Also found in the secret room


 * Airfield
 * Weapon Modification: Reload – While still in the sewers immediately upon arrival from the helipad via the sewer passage, there is a pipe to the right. The reload modification is inside this pipe.
 * Weapon Modification: Recoil – Inside the northeast tower (across from the electrical hazard zone)
 * Weapon Modification: Clip – In a crate in the electrical hazard zone
 * Weapon Modification: Accuracy – In a crate in a elevated shipping container southwest of the barracks. Accessible via the jump path (see annotated map)
 * Weapon Modification: Scope – In the secret room in the barracks, opened by activating a brick on the ground to the left of the dart board


 * Hangar
 * Weapon Modification: Recoil – Sold by the mechanic (400 credits)
 * Weapon Modification: Accuracy – In a crate inside the semi-trailer
 * 747 Airplane
 * Augmentation Canister: Ballistic Protection / EMP Shield – In the cargo hold, locked in a container (keycode: 9905)

UNATCO Headquarters (second visit)
The mission begins on Liberty Island near the entrance to the headquarters. The shed in the satellite communications compound is still accessible by the code 0451, and contains a repair bot that is useful for recharging energy.

Speak to Joseph Manderley inside the headquarters to learn that Paul Denton has been fired from UNATCO because he has not reported back since his last mission. Manderley then gives you a new assignment, which is to locate an airfield where the NSF has moved the Ambrosia. Before leaving for Battery Park, you may wish to pick up any useful equipment lying around the headquarters. Talk to Sam Carter to receive an accuracy modification.

Battery Park (second visit)
The subway station has a phone booth that opens the path to the next destination. The phone booth requires a code to activate. If you received the password "underworld" from the bum in Hell's Kitchen, you may get the code from Curly, who is found in the shantytown outside of the subway. If you do not have the password, you may buy it from Harley Filben in the subway. Alternatively, in one of the houses in the shantytown, there is a locked chest containing Curly's journal, which reveals the code (6653).

Brooklyn Bridge Station
The objective here is to find the secret passage to the Mole Tunnels. Details of the secret passage can be obtained by speaking o Charlie Fann and completing his mission.

Charlie Fann will give you a new secondary goal to restore the water to the homeless. Water can be restored by activating two valves in a utility room at the north end of the tracks, but this room is blocked by a cave-in. The cave-in can be cleared using an explosive, such as a LAM. Once you've cleared the cave in, activate the valves in the utility room and return to Charlie, who will give you the code 5482 for the keypad under the sink in the women's restroom. Use the keypad to open the secret passage.
 * You can obtain a LAM from Lenny, who is in the men's restroom. Purchase Zyme from Rock (the drug dealer at the corner). Then, talk to Lenny and give him the Zyme in exchange for the LAM.
 * Alternatively, you can obtain a LAM from El Rey, the leader of the Rooks gang upstairs. He will sell the LAM at a high price (750 credits), but will give it to you for free if you kill Rock. Speaking to El Rey actives an optional secondary objective to kill Rock.

Mole Tunnels
Unlike the Brooklyn Bridge Station, the tunnels are occupied by NSF terrorists, who use the tunnels to move supplies. The objective here is to find a secret passage that will lead to LaGuardia Airport.

Speak to the mole person Kevin Bradley in the settlement, who reveals that the local NSF leader can be found in a secret room activated by a brick mechanism. The brick can be found at the south end of the area, inside an NSF shack hidden behind cardboard boxes. Activate the brick to open the secret room. Talk to the commander, who will surrender without a fight, and take the NanoKey on the desk which opens the men's restroom.

The restrooms are at the other end of the area. Use the NanoKey to open the men's restroom, and proceed to the LaGuardia Helibase.

Helibase
Your starting position is somewhat far from the objective destination. To get there, you must first traverse through a series of obstacles. The first set of lasers (in the path to the left) can be jumped over by stacking crates. Later, you will come across patrolling security robots, which can be avoided by taking cover in the rubble nearby. Note that all turrets and robots can be destroyed using grenades or the GEP gun.

Eventually, you'll reach the main part of the compound, where you will find a stolen Ambrosia barrel that is guarded by NSF troops. Locating the Ambrosia will trigger the secondary goal of finding the two other stolen barrels, which are found later in the mission after you leave the helibase. The stairs to the left lead to the helibase control room on the second floor. Inside the control room, there is a switch near a potted plant at the SW corner that opens a secret room, which contains an augmentation upgrade canister and other loot.

The main objective is reach the interior helipad (the room with the helicopter inside), which is directly accessible from the control room. Note that helipad is guarded by a sniper watching from above. From the helipad, there are two paths that you may take to the airfield above: The sewer route gets you directly where you need to be (i.e., the boathouse) and allows you to pick up a reload modification along the way. However, you may take asphyxiation damage from the swim if you do not have aqualung or points allocated to swimming.
 * Elevator route – One option is to take the elevator directly to airfield. On the ground level of the helipad, follow the "exit" sign to an elevator, which takes you to the airfield.
 * Sewer route – The second option is to enter the airfield through the sewers, via a manhole located at the SW corner. The sewers path leads to the water near the boathouse.

Airfield

 * For additional details, please see the annotated map in the infobox of this article.

The airfield is guarded by security robots and watchtowers with camera-activated turrets. Each watchtower has an interior area with loot. Two of the towers have weapon modifications inside. One tower has a GEP gun inside. Turrets can be destroyed using explosives. However, if you do not wish to deal with the turrets at this time, you may still loot the towers at the end of the mission when all defense systems will be deactivated.

Once you've arrived, you will receive orders to assassinate Juan Lebedev, a high-ranking NSF member. The ultimate destination is the large aircraft hangar. However, the hangar can only be accessed from the barracks, which is locked behind the east gate. To get past the east gate, you must get to the boathouse, where the NanoKey to the east gate is found on top of a metal crate. If you took the sewer route, you will begin near the boathouse. Otherwise, you must trek through the robot defenses and NSF guards to get there. The boathouse also includes the second Ambrosia crate. Additionally, the NSF guards outside the boathouse carry the NanoKey to open the doors to the watchtowers.

Once you've obtained the NanoKey for the east gate, open the gate and proceed into the barracks, which is guarded by several NSF members. Note that to the left of the dartboard, there is a brick mechanism that opens a secret room. On the second floor of the barracks, there is a door to the hangar, opened by the code 5914.

Hangar and 747
Once inside the Hangar, you will encounter Paul and learn that he was part of the NSF all along. Paul asks that you speak with Lebedev and hear what he has to say.

Lebedev is inside his 747. The lower level (cargo hold) of the aircraft includes the third and final Ambrosia barrel, as well as an augmentation canister in a locked container (code 9905). The upper level of the aircraft contains the NanoKey to the front of the aircraft, where Lebedev is located.

Speak to Lebedev, who surrenders and tells JC Denton more about the conspiracy. Lebedev tells JC that he was created by a secret organization crazed for power, and that the same corporation that manufactures Ambrosia also created the Plague. At this point, Anna Navarre will require that you kill Lebedev, as ordered, or she will kill Lebedev herself. The options are: kill Lebedev, allow Anna to kill Lebedev, or kill Anna. Afterwards, UNATCO will take over the airfield and disable all defenses, allowing you to pick up any loot that you left behind. Head to Jock's helicopter to complete the mission.
 * If you kill yourself Lebedev, you will earn no bonus skill points. However, Manderley will be pleased with your actions.
 * If you allow Anna to kill Lebedev, you will earn 175 skill points.
 * If you kill Anna and Lebedev does not die, you will earn 200 skill points when you speak to Lebedev again. Lebedev will then tell you more about the conspiracy, and will name the organization behind it all, Majestic 12, a group powerful enough to control the United Nations.