JC meets with several of the homeless residents in Battery Park. They give him a password to a hideout for the "mole people", a group of homeless residents who live deep underground. JC also finds Harley Filben in the subway station, who gives him the code to a nearby keypad that will allow him to travel to an unused and abandoned subway station that connects to the airfield.
Once underground, JC enters the station and finds it filled with junkies, prostitutes and a street gang called the Rooks. After helping one of the denizens clear a route through some debris so that the water supply can be turned back on, JC obtains a code to the mole people hideout and exits the station through a hidden passage in one of the station's washrooms.
The mole people hideout is filled with NSF forces. JC manages to get through them and is informed by the residents that the commander has a secret room. Entering through a hidden door, JC finds a scared commander who begs him to stand down. He tells JC that they have no wish to be violent, and gives him a key to access a passageway to the helipad at the other end of the hideout. Once JC leaves, the formerly-hostile NSF troops become passive and ask him not to shoot.
JC continues through the passageways, past a pair of patrol robots and into a private terminal below the airfield, where he discovers one of the missing Ambrosia barrels. He eventually finds and uses an elevator to get to ground level and exits into the airfield itself, which is swarming with bots and NSF troops.
JC makes his way past and finds the second barrel, then heads through the guard shack to the inner hangar. Inside, he finds... Paul, who orders him to stand down, and reveals that he has been working for the NSF.
An incredulous JC asks what's going on, and Paul tells him to get on the nearby 747 plane and speak to Lebedev so that they can leave. JC expresses indignation at Paul's actions. Paul insists that there's a good reason for it, and they debate the ethics of his actions leading to more violence.
Onboard the 747, JC finds the last barrel of Ambrosia and confronts Lebedev, who tells him to respect UNATCO's policy of apprehending unarmed prisoners. Anna arrives suddenly and congratulates JC on completing the mission, then orders him to either execute the prisoner, or leave and let her do the dirty work. With Anna warning him not to disobey orders and Lebedev promising to reveal more information on his parents only if Anna leaves, he is caught at a crossroads what to do.
If JC shoots and kills Anna, she explodes as a result of her nanoaugmentation technology. Lebedev asks JC who he really is, and when he doesn't answer, Lebedev tells him that his parents were murdered precisely because they knew the answer to that question. He tells JC to go back to UNATCO and play along, and says that there is a much larger conspiracy at work. A horrified Alex wipes the records of the last few minutes as JC leaves so that Manderley won't find out what happened to Anna.
JC exits the 747, only to find Paul gone and UNATCO troops patrolling the area. They inform him that the airfield is secured. JC finds Gunther near the helipad, and feigns ignorance when asked where Anna is. JC gets back on Jock's helicopter and heads back to UNATCO.
Back at the base, Alex informs him that Manderley was listening in when JC spoke to Paul at the 747, and that it really is all over for the latter. In his office, Manderley blows up at JC and says he doesn't believe the story about Anna's death, then threatens serious repercussions if he's in league with Paul. JC insists that he's not, and Manderley informs him that they've activated Paul's "killswitch", a device implanted in him that causes flu-like symptoms and, eventually, death within 24 hours. Manderley orders JC to head to Hong Kong and begin liaising with the local triads to find out more about what Paul was doing.
If JC kills Lebedev, Anna congratulates him on being a true loyalist, while Gunther later commends him on doing what's necessary. Back at UNATCO, when Alex brings up Paul's defection, JC states that killing his boss should make his allegiance clear. Manderley is much more conciliatory towards JC in his mission briefing, but Paul's killswitch is still activated and JC is sent to Hong Kong.
If JC leaves Lebedev to Anna, she executes him, and Gunther says he will congratulate her. Alex is sympathetic towards JC's situation, but Manderley is not. JC then parts ways with UNATCO on somewhat sour terms for the Hong Kong mission.
Before he leaves, JC tails Walton Simons down to the base's jail and watches as he interrogates a pair of NSF soldiers captured during the Liberty Island raid. When one of the soldiers refuses to give up any information, Simons executes the prisoner and angrily tells Denton to leave.
JC heads back to the helicopter, but Jock tells him that they're instead going to Hell's Kitchen because Paul wants to meet him at the hotel. With that, they head back into the city...
- Boss Battle: Anna can become an impromptu one if you choose to fight her instead of killing Lebedev.
- But Thou Must!: Notably averted. Anna is forcing you to kill Lebedev, but he won't give up the required information until Anna leaves. The game makes it seem as though Anna is still invulnerable like in previous missions. However, you can kill her instead of Lebedev, and an entirely different sequence follows where Lebedev reveals crucial information to JC, while Gunther, Alex and Manderley's conversations change for the rest of the mission.
- Chekhov's Gun: If the bum that was being harassed by the gang members at the court in Hell's Kitchen was rescued, JC can learn the Mole People password for free and get Curly's blessing to enter it instead of having to pay Filben for the same information.
- Developer's Foresight:
- Harley Filben has alternate dialogue if you didn't speak to him at all during the Liberty Island mission, and his demeanor is much more cold and uncaring. Alternately, if you killed the NSF commander in the opening mission, Filben will give JC hell for killing one of his contacts.
- If you decide to kill all the Rooks except for El Rey in the abandoned subway station, leave him to run around until he becomes passive again and then talk to him, there is an alternate conversation where El Rey urges JC to be cool. JC subsequently threatens him and either tells him to go back to school (while receiving the LAM), or tells him he wants more (causing El Rey to throw the LAM at you and start running). If your inventory is full when you ask for the LAM, JC has a unique response where he chuckles and tells El Rey to wait a moment.
- Alternatively, you can do El Rey's quest to kill a rival drug dealer. If you should decide to just knock out the dealer instead, El Rey will complain about it before giving you the LAM anyway, while JC stresses that he used "the minimum amount of necessary force".
- If you turn on the water valves before talking to Charlie Fann, he has alternate dialogue expressing admiration for JC's discovery, while the latter claims that he was "just looking around".
- If you kill the NSF commander (via discovering his secret room) in the abandoned subway tunnels before doing anything else, JC has additional dialogue with a young boy if you haven't talked to him yet. The boy tells JC the secret of how to access the room, and JC then tells him not to go near it because it's "not too pretty in there".
- There are different commlink messages from Alex Jacobson depending on how many/which barrels of Ambrosia you've found, even if you leave the one in the underground airport terminal (which is nigh-impossible to do because the trigger for it activates almost as soon as you enter the main hall) for last, doubling back only after you've found the container in Lebedev's plane.
- When you discover that Paul is working for the NSF, he asks you not to shoot any of the (now identified as friendly) unarmed NPC's standing around the plane. If you do, he chews you out for it.
- When you are about to arrest Lebedev, Anna storms in and orders you to kill him. If you decide to kill her instead of Lebedev, you get an entirely new cutscene, where Lebedev informs JC that his parents were lab technicians, Alex will delete the audio transcripts of the prior few minutes and JC ends up lying to Gunther to cover his whereabouts during the shooting. The fact that nothing in the game clues you in to this makes it all the more shocking when it actually works. Killing Anna also impacts the rest of the game: when you're captured by the conveniently invincible Gunther Hermann, he gives you a special message about making you pay for her death after you escape confinement. Also, Navarre stays dead for the rest of the game, meaning the boss battle is skipped.
- The Anna encounter also has another variation. If you plant a LAM outside of the room you meet Lebedev, then listen in the background, she's blown to bits not long after Lebedev surrenders. By skipping the dialogue with her before she orders you to kill Lebedev, the same events happen, but J.C. tells Manderley that Lebedev booby-trapped the room, and Gunther will instead cotton on that you killed her later, as you are escaping UNATCO HQ.
- After completing the mission, the player can go back into the Laguardia Terminal near Jock's helicopter (down the elevator), where UNATCO soldiers have been deployed, and they will tell JC about their recovery operation of the Ambrosia (even subtly telling him he's not welcome anymore if he persists in his questioning).
- Did Not Die That Way: JC was told that his parents had died in a car crash. If Anna is killed, Lebedev reveals that they were executed because of their knowledge of JC's true heritage.
- Disc-One Final Boss: Lebedev.
- The rank-and-file troops at UNATCO (besides Corporal Collins) seem a lot more... distant and formal towards JC.
- Scott (the UNATCO soldier at the front desk of the base) mentions that Manderley sends agents he isn't sure about to Hong Kong...
- Dull Surprise: Invoked in-universe. When Lebedev drops the Wham Line about JC's parents if Anna is killed, JC has very little reaction, instead commenting that both he and Paul suspected as much when they were growing up.
- Gameplay and Story Segregation: You can massacre all of the (friendly) UNATCO troops in Battery Park and at the airfield before leaving (and after it's secured), but Manderley isn't concerned with their deaths so much as Anna dying on the jet, and it's never referenced again.
- Good Cop/Bad Cop: Depending on how the interrogation with the prisoners is conducted in the UNATCO basement, JC can play the "good cop" role against Walton Simons. Inverted if the player executes the prisoners themselves — Simons calls out JC before angrily telling him to leave.
- Heel–Face Turn: All of the NSF troops in the Mole People's hideout become non-hostile (and even scared of JC) when the commander agrees to stand down.
- He Knows Too Much: An unused phone conversation that was programmed into the game (and restored by mods like Shifter) has Tracer Tong attempting to advocate to Lebedev that JC should be executed due to his knowledge of the conspiracy, with Lebedev arguing that Paul vouches for him.
- Hidden Supplies: Both Laguardia Terminal and the adjoining access building into the hangar have hidden rooms filled with supplies, which can be accessed by triggering hidden switches. The subway station near the Mole People tunnels also has a hidden cache with a datapad and some flares on the upper level, at the opposite end of the hallway where El Rey is located.
- Hypocrite: Unless JC was Just Following Orders, Manderley chews him out for either refusing to kill Lebedev or letting Anna get killed (or so he thinks). This belies the fact that he was the one who authorized the mission in the first place, knew Anna was bloodthirsty and still sent a rookie (still on his first day on the job) along with her.
- Just Following Orders: Convincing the NSF commander to stand down in the Mole People tunnels will cause several of the terrorists (who will no longer attack JC unless provoked) to reference this trope by name, claiming they were just following the requests of their commander.
- Killer Cop:
- Anna tries to force JC to kill an unarmed prisoner (Lebedev) who has surrendered, and if he doesn't do it, she executes him herself.
- Simons (or JC himself) can fulfill this role during the interrogation of the NSF prisoners at UNATCO HQ.
- Man Behind the Man:
- In a rare heroic example, Lebedev is the one who convinced Paul to join the NSF, as well as being the one to distribute Ambrosia to people suffering from Grey Death and organized the NSF resistance in New York. UNATCO is painting him as the ultimate mastermind of the NSF so he will be taken out quickly.
- Lebedev's role extends to the expanded universe, where his company (Lebedev Global) employs several characters, including Anna Kelso and Alex Vega, and he plays a key role during a meeting to recruit Adam Jensen into the Juggernaut Collective in 2029.
- Multiple Endings: Onboard the jet, the player can either choose to kill Anna, kill Lebedev, kill both of them or leave the jet altogether. Doing so alters the conversations for the rest of the mission.
- My God, What Have I Done?:
- Subverted. Alex has a freakout if the player kills Anna on the jet and agrees to falsify the records, but later freaks out that they're going to be caught and executed for treason. JC is much more stalwart, and pointedly tells Alex that Anna was "Out. Of. Line."
- Conversely, if the player killed Lebedev, Alex has the inverse reaction — he starts to feel disgusted by himself for supporting the killing of an unarmed combatant, and makes some of those concerns known to JC.
- Off the Rails: Anna becomes too overzealous and orders JC to kill an unarmed prisoner. No matter how Lebedev is dealt with, it causes Manderley to lose trust in JC and send him on a mission to prove himself.
- Pinball: Used as part of a hidden secret — if you take the time to try to "play" one of the pinball machines in Laguardia, it will open a hidden room with supplies stashed by the NSF.
- Properly Paranoid:
- Speaking with one of the children in the Mole People tunnels (the one who greets JC by saying, "You're the spy, huh?") outright tells you that the "metal men" knew JC was coming, and informs him of the traps yet to be encountered on his route.
- Lebedev clues JC into the fact that there's a much larger conspiracy at work, and to keep his eyes and ears open when he goes back to work.
- Ambient dialogue with two of the NSF soldiers in the tunnel (securing an alarm near the bathroom exit) suggests that Paul was not only aware of JC's pursuit of him, but had the NSF specifically install boobytraps just to slow him down.NSF Soldier #1: They really think he'll make it this far?NSF Soldier #2: Paul said not to take any chances.NSF Soldier #1: Well, I guess he would know.
- Punch-Clock Villain: The NSF commander in the mole people hideout reveals that he's a reserve member who works as an accountant by day.
- Reassigned to Antarctica: Mere hours into his first day on the job, JC is sent to Hong Kong by Manderley, ostensibly to "find out more about the Triads," but said in e-mails to have been decided on because Manderley doesn't trust him anymore.
- The Reveal: Paul is working for the NSF, UNATCO isn't as squeaky-clean as JC thinks it is, and Anna has gotten a bit... overzealous with her duties.
- Self-Destruct Mechanism: Anna has a built-in explosive that detonates when she dies, reducing her (and anyone in the blast zone) to gibs.
- Sequence Breaking: You can kill Anna with LAM's by lacing the hallway leading to Lebedev's bedroom with them. She doesn't get the chance to speak before she's blown to smithereens.
- Story-Driven Invulnerability: Averted. Despite it looking like you won't be able to, you can kill everyone on the level besides Paul and Gunther, up to and including Anna and friendly NSF and UNATCO troops.
- Tainted Veins: Simons has bioelectric marks on his face, and it's revealed in a conversation with Reyes that he gets constant headaches as a result of his implants.
- Take a Third Option: It initially appears that the only things you can do are either follow Anna's order and execute Lebedev, or leave the jet and let her do it for you. However, there is another way - taking out Anna results in a new cutscene where Lebedev begins to reveal the extent of the conspiracy and tells JC to keep his eyes open.
- Wham Line: Lebedev's jet.Paul: That's right, JC. I'm working for the NSF.
- Followed by:Lebedev: Your parents were murdered precisely because they knew the answer to that question.
- Followed by:
- What the Hell, Hero?:
Simons: Jesus Christ, Denton!
- Paul chews you out if you decide to shoot the (now-friendly) NSF troops in the hangar.
- Manderley gives JC an epic rant if the player chose to kill Anna instead of Lebedev. He gives an even bigger one (and nearly fires JC) if both Anna and Lebedev are dead.
- Simons will call out JC if the latter intervenes in the interrogation of the NSF prisoners.
- You Have Outlived Your Usefulness: Simons will execute the NSF prisoners once it becomes clear that they refuse to play ball with his interrogation. Depending on how the conversation proceeds, the player can also question them to glean more information about the NSF's motives.