Jock drops JC off outside the gates of the Brooklyn Naval Shipyard. He heads in and finds two guards patrolling the gate, and responds that he's part of Bob Page's group. They warn him that they have orders to shoot on sight, but allow him to pass through unchallenged.
Inside, JC finds security bots patrolling the perimeter and members of the maintenance crew complaining about the terrible conditions at their workplace. He continues searching and comes across correspondence from Simons about his takeover of the base and demolishing of the Versalife building as a result of their security breach. JC eventually finds the entrance to the sub pen and heads inside.
A soldier at the front desk recognizes JC from the description given by the contact in Hell's Kitchen, and gives him some information on the sub. It is being held by MJ12 troops and loyal crewmen. The soldier gives JC a key to the loading ramp, and the agent boards the ship.
On the upper levels, JC finds a message relayed from Walton Simons to Captain Zhao stressing that he doesn't want any delays in spraying the virus. JC also finds a sample of Ambrosia and a key to the lower levels.
Below decks, JC sneaks around the ship and uses explosives to destroy several key weld points throughout the superstructure. The ship begins to buckle and shake, and Tong tells JC to escape. Once he's clear of the ship, Jock radios to inform him that Gunther executed a raid on Smuggler's hideout, but that the arms dealer wasn't found and the German agent left frustrated.
JC boards the helicopter again and they head to Dowd's hideout on the east side of New York. The helicopter touches down at a cemetery and a groundskeeper comes out to open the gate for him. Questioning to himself why someone would be out this late at night, JC kills the groundskeeper and inadvertently destroys a nearby generator.
In a nearby crypt, Dowd thanks JC for bringing him Ambrosia and relays some of the Illuminati's history. He tells JC that Beth DuClare is dead, and that the agent will instead have to search for her daughter, Nicolette, in Paris. He also tells JC to seek out and find the terrorist group Silhouette, who have taken refuge from MJ12 in the Paris catacombs. When he asks about the gatekeeper, JC tells him he already killed him, prompting Dowd to comment on how Properly Paranoid the agent has become.
Dowd relays some additional information about Page's past as an Illuminatus and his split from Everett before Jock radios JC and tells him to hurry up - an MJ12 assault team has arrived. JC dispatches the troops and tells Jock that they're going to Paris...
- Bizarrchitecture: The tunnel next to to the fan leading out of the upper vents in the shipyard is a futuristic-styled place with swirling walls, a gap in the floor and a horde of spiderbots at one exit, and looks completely out of place next to the drab fan room and the tunnels leading down to the dock. It's possible that this may have been repurposed from the cut "moon" level.
- Carrying the Antidote: The medical lab onboard the Wall Cloud just happens to have a vial of Ambrosia, which can be given to Dowd after the mission. However, it's not mission-critical, and not getting it only results in some alternate dialogue with Dowd afterwards.
- The Coup: Enemy Chatter onboard the supertanker reveals that Simons is trying to enact a bloodless coup by enacting several executive orders at once.
- Crazy-Prepared: One of the soldiers in the command centre of the Wall Cloud is able to recite executive orders by number, and is well aware of how and when Simons will enact his coup.
- Crusty Caretaker: The caretaker at the Lower East Side Cemetery, who turns out to be a spy for MJ12.
- Developers' Foresight:
- The two guards at the front gate of the shipyard actually have alternate dialogue once the ship is destroyed (despite there being no reason for the player to trek all the way back there), though this is a simple change to "I don't have time to talk".
- The two mechanics by the Wall Cloud also avert this — their dialogue never changes from the "we're rooting for you/I want to know what's on that boat", even after the weld points are destroyed and the boat is collapsing.
- If you kill the caretaker before talking to Dowd in the crypt, he will comment on how Properly Paranoid JC has become.
- Disproportionate Retribution: According to an email found in Simons' office, the Versalife building was demolished after JC infiltrated the labs.
- Dummied Out: There are lines that were originally meant to be said by the Chinese troops onboard the Wall Cloud if JC is allied with UNATCO. These are remnants of a deleted subplot where the player could have stayed loyal to the company instead of working against them.
- Interface Screw: The camera constantly shakes and jostles after all of the Wall Cloud's weld points have been breached, and only stop when JC clears the immediate dock.
- Mistaken Identity: While the rank-and-file troopers at the shipyard will shoot on sight, several of the mechanics and dock workers mistake JC for a member of Bob Page's team, and will cheerfully tell JC about how much they don't like Simons and are confused by what's going on. You can even help one of the mechanics aboard the ship with a wiring problem!
- The Mole: The caretaker at the cemetery is really working for MJ12.
- Properly Paranoid: Dowd can give the player this reaction if they kill the groundskeeper before speaking with him.
- Self-Destruct Mechanism: Deconstructed. The act of destroying the ship is played as straight as possible, with the player being tasked to destroy five weld points throughout the ship (one of which is hidden behind a large wall and normally inaccessible beyond throwing a LAM over it) and activating the bilge pumps before the ship breaks. Even then, Tong tells JC that it will take 30 minutes for the ship to break apart.
- Stealth Hi/Bye: Dowd disappears as soon as JC exits the crypt, and there's no way to find him again.
- Take Your Time: Despite Tong's hurried remarks that JC needs to escape as soon as possible (and the constant shaking of the screen), there is no rush for the player to leave the exploding ship.
- Villain Ball: The troops guarding the front gate of the shipyard take JC at his word that he's part of MJ12, and say that although they have orders to shoot anyone who tries to come in, they still allow him to pass through if he has a key.
- What Measure Is a Mook?: The player can find emails to Captain Zhao from his daughter saying how much she loves him and wishes he'd come back home soon. Then you find a holocomm message from Simons warning that there shouldn't be any delays before the Grey Death is sprayed on the East Coast.