JC wakes up without his possessions in a fortified jail cell at an unknown location. After surveying his surroundings, a mysterious individual named "Daedalus" contacts him on the infolink and tells him that he is cutting power to the area and opening the door for him to escape.
He exits the cell and beats a nearby guard with a melee weapon, then retrieves a pistol. Daedalus informs him that he is in a secret MJ12 base underneath UNATCO headquarters, that Paul is alive and in an infirmary to the south, and that at least one of the Denton brothers needs to escape alive. JC sneaks through a nearby robot maintenance bay and into the base's armory to retrieve his weapons and items.
Heading back where he came from, JC heads down another wing and comes to the Medical Labs, and dispatches several troops and high-ranking Men in Black operatives on his way. He encounters several doctors sympathetic to his cause, and eventually finds Paul being studied by amazed doctors in the infirmary.
Paul tells him that he was captured as well, and that the doctors are studying the effects of the killswitch. He thanks JC for finding him, and says that he will be able to slip out on his own and get out of the city with Smuggler's help. Paul also implores JC to be mindful of the people he comes across in the UNATCO base above, because many of them are Just Following Orders. He finishes by telling JC to find a man named Tracer Tong when he gets to Hong Kong.
Daedalus provides an exit code for the base's door, and JC subsequently exits into Reyes' office. The shocked doctor tells JC that Manderley informed the staff that he was dead. JC says that he's heading out, but indicates that Reyes can slip out afterwards and find Tong in Hong Kong as well. Reyes thanks him, and gives him an augmentation canister he was planning to surprise JC with a graduation present.
At the armory, JC meets Carter and attempts to explain what is happening, but Carter refuses to listen and simply opens the door. He tells JC to load up before he breaks out, and says that UNATCO will get things back on track eventually.
In Alex's office, JC states that he's thankful to him for helping to spring him out, but Alex claims he has no idea what he's talking about. JC then asks if he's Daedalus, and Alex says he's never heard of him, but that he'll do some research and see what he can find. JC finishes by telling Alex about how to find Tracer Tong in Hong Kong, and Alex pledges to seek him out afterwards.
Upstairs, JC finds several hostile soldiers (and Anna Navarre, if she's still alive) and dispatches them, and enters Manderley's office to Janice Reed's shocked bewilderment. After seeing Manderley having a video conference with Simons, JC shoots and kills him. Simons shrugs Manderley's death off and comments that it has no bearing on his plans, and states that JC only has 18 hours left on his killswitch.
Upon exiting the base, an angry Gunther radios JC and tells him that he will make him suffer for Anna's death. Jock is at the nearby helipad, and says that he was asked to fly to the base by Daedalus. JC then tells him about Tong, and Jock mentions that he knows where the compound is.
The helicopter sets off one last time from UNATCO...
- Badass Boast: If JC kills Manderley before initiating the conversation with Simons.JC: Since that makes you my new boss, take a good look at Manderley's dead body. Consider that my resignation. I don't have time to write a letter.
- BFG: A Plasma Rifle can be found in the MJ12 Armory, and vaporizes anyone unfortunate enough to be in its way.
- Conspiracy Redemption: Nearly all of the major staff members (besides Manderley, who is corrupt, and Carter, who thinks he and others can help put the organization back on track) finally realize that JC was right about UNATCO's affiliation with MJ12, and Reyes and Alex decide to join the resistance in Hong Kong.
- Corrupt Corporate Executive: Manderley is simply a corporate mouthpiece brought onboard by Simons because he was agreeable to FEMA's orders.
- Developer's Foresight:
- If you visit her in the UNATCO break room while you're breaking out, Shannon will admit to you that she's the one who's been stealing weapons and ammo from the armory. She'll also offer to sell you scrambler grenades. If you then go back to Sam Carter (or talk to Shannon before seeing him) and talk to him, despite having no reason to go back there, JC will inform him who the armory thief was. Carter will then reveal there's more to the story than you know, and Shannon's gonna be facing an ugly surprise in the morning.
- The dialogue with Walton Simons changes during the escape if you kill Manderley before triggering his conversation (which is usually done by tossing a LAM or firing a rocket into the room before you enter). Simons brushes the death off and says Manderley was expendable, before commenting that it has no bearing on his plans.
- If you choose to spare Anna in the Battery Park Subway Station and during the escape (the latter by using exploits to get past a locked door), Gunther has alternate dialogue reflecting this fact when you're heading out of UNATCO's front door ("I regret that we only worked together once."). He even has an alternate line tied into this decision, based on whether you chose not to give him a weapon during the first mission.
- Dull Surprise: Anna Navarre (if JC uses her killphrase) says "How did you know...?" in a pretty deadpan voice, even though she's fully aware she'll be blown to bits a mere second later.
- Dungeon Shop:
- One of the mechanics in the MJ12 Robot Maintenance Bay will offer to sell a handful of items to JC, including some ammunition and the security login.
- The fact that UNATCO is under a lockdown and soldiers are hunting for JC doesn't stop Shannon from offering to sell him high-end scramble grenades.
- Face–Heel Turn: All of the rank-and-file UNATCO troopers turn hostile, and won't hesitate to shoot JC upon seeing him.
- False Reassurance: Simons tells Manderley that the latter has a desk job waiting for him at the Library of Congress. Later on, you find out that Manderley was (presumably) executed off-screen for his failures if the stayed alive during the escape.
- Gameplay and Story Segregation:
- Manderley is always treated as dead if he is dealt with before talking to Simons, even if the player knocked him out before initiating the conversation.
- Likewise, even in the (unlikely) event that the boss battle with Anna is skipped, she's treated as dead for the rest of the game.
- Hero Antagonist:
- After defecting from UNACTO, any UNATCO trooper, cop or soldier that's not part of the conspiracy or sadistic is this.
- Even Corporal Collins (who was the only person who called JC by his first name rather than an informal rank) and Scott (the receptionist at UNATCO's front desk, who went to the same academy as JC and defended his actions in Hell's Kitchen) have no qualms about pulling out their assault rifles and unloading into him if he gets within eyesight.
- Hope Spot: A rare villainous example. Before JC enters Manderley's office, the latter is speaking to Simons (who has apparently spoken with Page and agreed to give him a job in the Library of Congress). If JC kills Manderley, Simons reveals that he was expendable and that it has no bearing on their plans. If JC spares him, Manderley is presumably executed anyway.
- Humiliation Conga: In the span of just a few days, Manderley's plans fall apart around him. His top agent, Paul Denton, becomes a turncoat and starts assisting the NSF. His new recruit, JC, turns traitor as well and runs roughshod through the MJ12 base after he's captured. Despite his best attempts to keep them in line, he's ultimately viewed as expendable by Simons and Page. They give him a Hope Spot before letting him be executed by JC or (presumably) killing him themselves and framing JC for his murder.
- The Idealist: Carter is still convinced that UNATCO can be set back on track, even when JC tries to tell about how corrupt the organization is.
- In the Back: If he remains alive through the conversation with Simons, Manderley will pull a gun on JC the moment his back is turned. On the highest-difficulty level, this has a good chance of dropping the player in one shot.
- Kleptomaniac Hero:
- Subverted. Shannon is the only person besides Reyes, Carter and Alex who is sympathetic to JC's cause, and reveals that she's the office thief before offering to sell JC some powerful scramble grenades. However, if you go back to Sam Carter and tell him about what she's doing, he replies that he already knows and that they're going to punish her in the morning.
- Also defied by Carter, who orders JC to grab whatever he can carry on his way out of the building, while unlocking the armory door in the process. Rooting around the offices nets additional supplies in Alex and Jaime's offices and the UNATCO breakroom (though the ATM, unusually, has no funds available, unlike its previous visits).
- Questioning Jaime Reyes enough will lead him to tell you to take whatever you want from the medical wing, as he will be catching a plane in the morning and "(this) isn't my clinic anymore."
- Lockdown: UNATCO itself goes one into following JC's escape, necessitating that he obtains the key from Alex before he can open the impenetrable door that leads out from Level 2. By the time you reach Scott's desk at the ground floor of the building, his computer will note that an "active situation" is going on in the lower levels, necessitating the lockdown.
- The Man Behind the Man: Manderley is simply a puppet of Simons, who's the one pulling UNATCO's strings alongside Bob Page.
- My Country, Right or Wrong: Carter refuses to leave UNATCO, and tells JC that it can be fixed eventually by having good people reform it from within.
- No-Gear Level: Subverted. JC starts out in the jail cell with no weapons or items, but inexplicably still has all his ammunition and keys. Once you escape, you soon get a handgun and baton, and if you make it to the Armory, you can outfit yourself with some of the most powerful weapons in the game.
- Plasma Cannon: You can find a rare and powerful Plasma Rifle in the MJ12 Armory.
- Pre-Mortem One-Liner:JC: Take your best shot, flatlander woman.Anna: How did you know...? (explodes)
- Self-Destruct Mechanism: One of the ways Anna can be defeated in the UNATCO base.
- Skippable Boss: The fight with Anna can be skipped, but it is very difficult and has no real effect on the plot beyond an alternate piece of dialogue.
- Spanner in the Works:
- Daedalus, the apparent hacker who sprung JC from his jail cell and (as you find out later in the game, if his apartment is broken into) obtained the necessary clearances for Jock to fly a stealth helicopter to New York to pick JC up from UNATCO.
- Checking Carter's computer in the Level Three armory reveals an interesting message from someone going by the identity "Minister of True Lies", who thanks Carter for his help compromising UNATCO's security protocols and hypothesizing on Daedalus' identity. The "Minister's" identity will be made clear in a later mission.
- Swiss-Cheese Security: Even before JC was arrested, MJ12 was dealing with some containment breaches of their own, with a semi-secret area (accessed through the back of the Greasel Lab area) containing a pair of escaped specimens that fled through a vent at the back of the wing. A single security terminal can also alter the AI routines of the security robots to make them friendly to JC (and attack MJ12 troops).
- Talking the Monster to Death: JC can do this to Anna by discovering her killphrase and saying it to her before exiting the base.
- This Is Unforgivable!: Explicitly stated by Gunther when he finds out you killed Anna Navarre.
- Trailers Always Spoil: The original teaser trailer spoiled part of this mission, via the scene where Anna visited JC in his cell and says that she "came to watch him die" (that is, if she's still alive).
- Video Game Caring Potential: You don't get much for saving Miguel (the NSF prisoner in the MJ12 jail) besides a few skill points, and he's notoriously prone to dying easily, but it feels good to help him out. In certain mods like GMDX, the player will receive additional skill points for leading him all the way to the helipad outside the building.
- Video Game Cruelty Potential:
- You can choose to rat out Shannon to Carter, even though she is one of the few people helping JC and Carter already knew about her complicity in the office thefts. Conversely, you can also shoot and kill Shannon after she's sold you the grenades.
- You can fire a rocket or toss a LAM into Manderley's office as the latter is having a conversation with Simons. Manderley barely has time to stand up before he's blown to bits.
- Villain with Good Publicity: An issue of Millennium Magazine (with Bob Page's face on the cover) can be found in the MJ12 Medical Labs.
- Why Am I Ticking?: If Anna is still alive and JC uses the killphrase, she expresses confusion and realizes what's happened just before blowing up.
- With This Herring:
- Averted. The MJ12 Armory (after the initial risk of sneaking past two heavy military bots) has enough weapons, items and ammunition to make things much easier for the escape. Likewise, when you meet Carter, he opens up the UNATCO armory and tells JC to take whatever he can carry to aid in his escape.
- Interestingly, the UNATCO breakroom ATM (which had multiple accounts that could be looted for credits during each prior visit to the building) is left devoid of credits, which will make purchasing the scramble grenades from Shannon much more difficult if the player hasn't been pooling their cash up to this point.
- You Can't Thwart Stage One: In the event that Anna is still alive, Alex will refuse to give JC the key to the exit until he kills Anna, as he knows the latter would immediately know it was his fault and kill him. That being said, it is possible to bait her into opening the door without killing her, but the game presumes she is dead for the remainder of the plot, regardless.
- You Have Failed Me: Checking Manderley's computer shows an email from Simons to Manderley, placing blame on him for the failure of JC and Paul and the waste of resources.