Jock lands outside Area 51, which has had most of its exterior destroyed by the impact of the missile. JC climbs a nearby tower to dispatch a sniper, while Tong radios in and says that he is feeling well enough to help JC as Mission Control again. Tong tells him that the goal is to destroy the base once and for all.
Exploring the surface, JC is confronted once again by Simons, who comments on their frequent meetings like they're in a hall of mirrors. JC tells him that it must make him "one ugly son of a bitch" and finally kills the FEMA director.
Inside a bombed-out hangar, the agent finds a soldier who was hiding from a group of MJ12 troops and learns that there are multiple access points to get to the lower sectors of the base.
JC uses an elevator to travel down to Sector 2 and finds the base's crew module. Everett appears and congratulates him for getting in. He tells JC that even though Tong wants to destroy Area 51, he believes that there is a better way — kill Bob Page and allow the Illuminati regain to the control of the world that was taken from them by Page. Everett also extends an invitation for JC to join the Illuminati, telling him that there is a seat for him at their council if he kills Page.
JC continues through the sector and finds several dead scientists, MJ12 troops and Men in Black. As JC waits for an elevator, Page radios him and insinuates that he is going to merge with Helios to become a god. He also goads JC about his (fake) parent's deaths and says that he is sending up the agent who did the job. JC confronts and beats a Man in Black and several troops, and Page once again taunts him by saying that he's faster on his feet than his father was.
In Sector 3, Tong appears to JC and tells him to ignore Everett's proposal. He says that the best way to deal with the base is to destroy it and let the world regress to a "New Dark Age" so it can rebuild without the reliance of technology under governments that is on a scale that humans can manage.
JC searches through an office and finds old emails detailing the origin of the cloning project that resulted in his and Paul's births. He is suddenly contacted by Helios, who refuses to allow him access to Sector 4 (where Page is residing) until the agent visits him.
He heads to the Aquinas Hub, and finds Helios in its core. The AI tells him that he doesn't want to merge with Page, but will merge with JC instead and create a new world ruled by artificial order and control. JC is confused as to why the AI would do such a thing, but it asks him to trust in what it's doing and says that it has activated various defenses in the base to help. It asks JC to deactivate several uplink locks in Sector 4 before he leaves.
Just before JC arrives at Sector 4, Paul appears on the holocomm and expresses surprise that he was able to get through. JC asks his brother what's happening, and Paul tells him that Helios has taken control over the infrastructure of Hong Kong and allowed traffic and free trade to begin again.
They have a conversation about which course of action is the best to take. Paul admits that he doesn't have an answer, but that he knows JC will do what's right and expresses hope for the future before ending the conversation.
In Sector 4, JC finds the remnants of the cloning project and several tanks with copies of Paul Denton (assigned the names of Alex Denton, Bob Page and Walton Simons). He avoids a trap set out by Page and continues through into a walkway, where Page is attempting to turn himself into a cyber-assimilated life form in an EMP-shielded chamber.
Page rails at JC for his antics and says that he will become a god soon, before turning the sector's defenses on the agent. JC is now faced with a choice of which course of action he should take...
Merge with Helios
JC heads through Sector 4 and deactivates the uplink locks in the Aquinas Router control room with Helios' help (192.168.0.1), despite Everett and Tong's pleading that he's not doing the right thing. Page ineffectually orders him to stay away until the transformation is complete. The agent returns to Sector 3 and meets Helios, who asks if he's ready. JC question the process, asking what will happen to him. Helios states that he will still, in some sense, be himself, but he will also become a part of something greater and be empowered to lead humanity away from darkness and unto a better path. JC briefly muses that perhaps this very moment was what he was created for in the first place and tells the AI that he is ready, stepping into the tower containing it. Back in his pod, Page desperately begs Helios not to leave him, but to no avail. The two entities are merged in a flash of light. Speaking in Helios' voice, JC announces that he's ready to help change the world...
New Dark Age
With Tong's help, JC deactivates the coolant running into the antimatter tanks in Sector 4. Everett and Helios both beg him to stop and say that it's not the right course of action to take, while Page expresses disbelief that JC would blow the base with everyone — including himself — still inside. JC heads back to Sector 3 and dispatches an engineer before activiating the failsafes and triggering three ion reactors. The chain reaction causes the entire building to begin exploding, and JC starts running out. Tong radios in and says that the world's infrastructure (and technology) are collapsing, and implores JC to find him in Hong Kong and help rebuild society. JC keeps running as a massive flash of light consumes the screen...
Kill Bob Page
Alex tells JC that if he wants to overload Page's chamber, he will have to deactivate four "fusion reactors" located around the sector. JC heads down to the lower levels and begins switching off the reactors, while Tong and Helios both tell him he's wasting time. JC also deactivates several mini-Universal Constructors that are producing Karkians, Grays and greasels. Seeing what JC is doing, Page begs for his life and tells him not to turn off the last reactor, but the agent does so anyway. JC turns off the forcefield around Page's chamber, which overloads it and kills him. Some time later, Morgan meets with JC in the Illuminati's headquarters, asking him how he is settling into the organization. JC explains that he is overseeing the distribution of the the vaccine, but it probably will take months for society and global infrastructure to normal like the old days. Morgan tells him that he will see to that the Illuminati's various front organisations are going be reactivated and resume their work of subtly influencing the various governments of the world. The way he sees it, the Grey Death might have caused quite a bit of chaos, but through their work, the epidemic and the riots that followed in its wake will soon be nothing but a faint memory. When JC questions what they've accomplished, Morgan explains that together, they lead humanity into the light from their place in the shadows, and this time they will do it right...
- Adaptation Distillation:
- Interestingly, the PS2 port, The Conspiracy, functionally changes the tone of the Illuminati ending by removing several of JC and Everett's lines (specifically, JC commenting that he's personally overseeing food distribution, and Everett saying that this time, the Illuminati have a chance to "do it right" via a "compassionate conspiracy"). As a result, JC's tone sounds more regretful and uncertain, while Everett is implied to be fulfilling the exact same role Page once did.
- Also from Conspiracy, the New Dark Age ending has a longer ending speech by Tong, who says that he never talked about his plan before, and (through the static) comments that the separated villages will focus more on "self-discipline, philosophy" and how the world will create "small states (with) genuine self-rule". Conversely, JC isn't shown attempting to Outrun the Fireball in this ending, instead showing him flinch as an automated voice mentions how the failsafes are no longer working.
- Apocalypse How: Destroying the Aquinas Hub knocks the world back into a new Dark Age as all global communication and commerce is wiped out. To quote Tracer Tong: "No more infolinks, no transmissions of any kind - we'll start over, live in villages." Destroying it doesn't directly cause more deaths, but humans have been dropping like flies since before the game begins.
- Apocalyptic Log: One especially depressing log (found beside a dead soldier wielding a LAW rocket launcher) details his Last Stand against attacking MIB's, who walk up to his dead body and shut off the recorder to end the log.
- Appeal to Flattery: If the player decides to shut down the fusion reactors, Page attempts to sway JC by offering him money, power, Versalife itself and a spot in President Mead's cabinet.
- Badass Creed: In the "Kill Bob Page" ending:Everett: We are the Invisible Hand. We are the Illuminati. We come before and after. We are forever. And eventually... eventually we will lead them into the day.
- Bizarrchitecture: The level transitions from a fairly old-fashioned military bunker/installation to a futuristic series of corridors with holoprojectors, an EMP-shielded control room, brightly-lit offices juxtaposed with dimly-red colored tunnels and a multi-leveled final area with little discernible purpose. Lampshaded by a datapad you find from a worker complaining that the site is a mix of old-school 1950's technology and futuristic upgrades installed by Majestic 12.
- Book Ends: In the "Kill Bob Page" ending, the shots of JC and Everett talking are identical to the same shots of Page and Simons talking in the opening cinematic. This is made even more blatant in the PS2 The Conspiracy port, where the imagery extends to the same wall of TV's both men are watching, and it transitioning into the hand statue at the end, as in the intro from the same port.
- Brain/Computer Interface: The existence of this technology is how Page is carrying out his final plan, and how the player can carry out the Helios ending. This is made much more explicit in the PS2 port, The Conspiracy, when JC's head shakes violently as the machine begins the upload process.
- Chekhov's Gunman: In the event that Paul is still alive, he will appear to JC just before the access point to Sector 4, and give a summary of JC's choices (while telling him that he trusts his brother to do the right thing). If he is not present, Savage will appear and provide a similar summary of JC's choices.
- Dare to Be Badass: During the Helios ending, when the titular machine explains how JC will become a half-human hybrid with the AI, the agent only thinks for a moment before giving his response.JC: This is what I was made for, isn't it? This is why I exist. Alright. Let's do this.
- Deadpan Snarker: When Page tells JC about his plan to become a god.JC: Does this mean I don't get the job?
Page: Already I'm more than human. Soon, I will be pure light! Pure energy! Helios and I! I will burn like the brightest star.
JC: You're gonna burn, all right.
- Dummied Out:
- Exploring outside the level boundaries reveals bits of architecture (including an oddly-textured window in a separate room from the map in Sector 2), suggesting there was more to the level.
- The mechanic in the Reactor Lab has variable lines based on how many of the Grays were killed]], along with a much longer conversation where he could muse on the purpose of the reactor itself (likening it to an antimatter bomb). The conversation doesn't normally play because the correct plot strings weren't set, but they were restored through mods.
- There is also an unused music track, which isn't titled, that has been suggested as being a "Departure" cue based around the original intended concept of a subsequent "Moon" level or an unused cue for a fourth ending (the potential "Side with Page" ending). In the GMDX mod, the music is restored and used as the combat theme for Sector 4.
- Several infolink messages were left unused, including a dialogue from Everett in Sector 3 or a final dialogue from Helios if the Merge ending were taken. Additionally, an unused portion of Tong's final dialogue with JC (in the New Dark Age ending) would have had him mention that all he can hear is "howling" from the Net as it goes offline.
- Elaborate Underground Base: Area 51 itself, which is comprised of four separate underground levels.
- Elevator Action Sequence: Though not held directly on an elevator, a difficult battle begins when a group of commandoes and an MIB ride up an elevator to attack JC in a small room with next-to-no cover.
- Everything Trying to Kill You: The final fight with Page is not a traditional boss fight so much as Malevolent Architecture mixed with Flunky Boss. On the three floors of the massive room in which he's being held, he's got swarms of repopulating minions (you can rush the nanoreplicators creating new creatures and turn their failsafes on, fortunately). He's also able to selectively blow up some of the computer banks and doors where you travel to block your progress.
- Fiction as Cover-Up: The Sector 2 computer with relevant emails to the game's lore mentions that The Grays are actually artificial life-forms that resemble the popular idea of aliens (round heads, gray skin) and is implied to let rumours about them circulate as a smokescreen (an in-game form of Memetic Mutation; even noted as such(!) in the email) for what they are really up to in the Area 51 facility.
- Fling a Light into the Future: An interesting variant found in Sector 2 — an employee named Julia Shears manages to copy data from the facility's servers to a computer while hacking Helios' archives. These emails contain highly-specific information regarding JC's past, as well as information regarding cloning efforts and the true nature of The Grays.
- Gameplay and Story Segregation: The endings seem to have been rendered before the last level was finalized. Characters ask things which they should already know. JC asks who and what Helios is (despite being directly responsible for its inadvertant creation). Bob Page asks what's happening, even though moments before he was begging JC not to overload the complex (in the "New Dark Age" ending). JC is implied to be only a few months old (based on the intro cutscene and the description of the clone tanks in Sector 4), yet both he and Paul know for certain that they were raised by parents, went to a formative school and graduated through UNATCO. JC asks the true identity of "The Organization", even though previous radio messages have clearly referred to it as The Illuminati. The Kill Bob Page ending has JC and Everett talking in Versalife, after it was already established in a previous level that the building itself was demolished by MJ12.
- Hellish Copter: If JC didn't alert Jock to the bomb at Everett's helipad, the latter goes down with his stealth helicopter and dies just after dropping JC off at Area 51.
- Hoist by Their Own Petard: Page's plan to uplink Helios with his own mind goes awry, once the machine intelligence starts thinking for itself. First, it improves the situation in Hong Kong by opening the roads and declaring the Triads illegal, then it asks JC to uplink with it directly. Depending on which ending is taken, Page is either last seen screaming at Helios in fury after giving it life, futilely asking where the AI is as the complex explodes, or asking what's happening as JC merges his mind with Helios.
- How the Mighty Have Fallen: Page goads Dowd (who sent a message to JC telling him to bring back the Illuminati) by comparing the latter (once a member of the Illuminati Council) to a senile old man having delusions.
- Kick the Dog: Page casually mentions the death of JC's parents multiple times throughout the level.Page: Barely a scratch. You're a little faster on your feet than your daddy was.
- Late to the Tragedy: JC and Jock arrive at Area 51 in the wake of the missile launch, which has caused damage to the surrounding area and resulted in MJ12 taking steps to secure the exterior, including the deaths of a group of soldiers and various scientists inside.
- Mook Maker: Area 51's inner depths have a few Universal Constructor outlet chambers that constantly generate enemies to throw at you, such as Greys. You have to find a switch to seal the rooms off to stop the reinforcements from coming in.
- Multiple Endings: Three distinct endings, each with their ups and downs.
- Merge With Helios: JC combines himself with Helios (who has already told him that it has the capabilities and knowledge necessary to regulate trade and rule the world).
- New Dark Age: JC overloads the base's antimatter reactor, which destroys everything inside and shuts down the world's infrastructure and technology.
- Kill Bob Page: JC disables the fusion reactors and overloads Page's containment field, killing him and letting the Illuminati step in to restore order (and led by Everett and JC).
- Nice Job Fixing It, Villain: Page's plan to merge with Helios backfires when the AI gains a conscience and begins operating on its own, first by restoring infrastructure in Hong Kong and then by sidestepping Page's plan by asking to merge with JC instead.
- Not Quite the Right Thing: Each of the three endings have net positive and negative traits, but by the time you get to the final sector, the player must take one of these options to beat the game: either restore the Illuminati and trust in Everett's ability to create a "compassionate conspiracy", merge with Helios in an attempt to govern humanity via machine AI, or destroy the facility and knock the world back to a functional "New Dark Age" and trust in Tong's plan of rebuilding the world through villages.
- Order Reborn: In the "Kill Bob Page" ending, the Illuminati return to power, led by Everett and JC.
- Outrun the Explosion: The "New Dark Age" ending has JC running to escape Area 51 before the antimatter reactor overloads and destroys everything.
- Retcon: As part of the Gameplay and Story Segregation of the final level not matching up with other parts of the game, an email explains that while JC is a clone, he grew up "normally" (that is, under the thumb of a corrupt corporation that had his parents murdered for not wanting to make him a lab rat), as well as implying that JC was sent to Switzerland for part of his education (to say nothing of apparent childhood memories he has of being engineered). The intro, on the other hand, implies that JC was an out-and-out clone that was activated, grown and deployed within six months (with Page saying to bring JC "online" while showing a shot of a clone being grown in a tank). Later works in the series outright state that JC was "born" (a clone embryo implanted in a donor who carried him to term) on March 17, 2029.
- Schmuck Bait: Subverted. If the player access the ventilation fan on the surface level, Page will call and tell JC, "Jump! You can make it!" This was likely because he is trying to goad JC into committing suicide by jumping through the ventilation fan. However, there's nothing stopping the player from destroying the fan and jumping down the vent, which skips all of Sector 1 and takes you directly to the Sector 2 entrance.
- Sequence Breaking: It's possible to skip the entire journey to Sector 4 (and skip straight to the New Dark Age ending) once you realize that due to an incorrectly-placed cover over the "final button" in the Reactor Lab (that's just big enough to be clicked on), you can activate the antimatter reactors when you first arrive.
- Shiny New Australia: In an attempt to bribe JC into stopping his dismantling of his plans, a desperate Bob Page promises him that he can have all of Europe as his own personal fiefdom.
- Skippable Boss: The fight with Simons (if he wasn't killed at the Ocean Lab) can be skipped by staying away from the crew quarters near the entrance to Sector 1.
- Snap Back: In the "Kill Bob Page" ending, Everett and JC are speaking in Versalife's lobby. This is despite the building in question explicitly stated to have been demolished by MJ12 in a previous mission. The Conspiracy, the PS2 port, changes this to be a different form of Book Ends by having JC and Everett speak in the same conference room where Page and Simons had their conversation in the intro.
- Snark-to-Snark Combat: JC's conversation with Page in Sector 4.
- Spanner in the Works: Initially, JC has to make a choice between killing Page or scuttling the entire facility... until Helios asks JC to merge with it in an attempt to create a higher intelligence. To that end, Helios functionally refuses to merge with Page and fixes the situation in Hong Kong by declaring the Triads illegal and reopening the roads for commerce to flow again.
- Swiss-Cheese Security: JC's infolink finally goes off the deep end, with numerous characters being able to listen and give advice, sometimes at competing or inopportune moments. It's revealed that Tong, Alex, Paul and Jock (if they're alive), Helios, Stanton Dowd, Page and Everett are all listening in at once, with Page at one point even responding to an infolink message Dowd broadcasts to JC about the return of the Illuminati.
- Tempting Fate: The engineer in the Sector 3 Reactor Lab expresses confusion and doubt that anyone would want to overload the reactors, commenting that it's a ridiculous notion to begin with. If the player actually decides to go through with it, the technician freaks out and pulls a gun on JC in an attempt to stop him from overloading the reactors.
- Villainous Breakdown: As he begins to realize that JC is ruining his carefully-laid plan, the normally arrogant and calm Bob Page first attempt to offer various increasingly desperate bribes to JC, before being outright reduced to inelegant begging and pleading for him to stop, regardless of which ending is taken.
- We Can Rule Together:
- In an effort to convince JC to abandon his plans and let him complete the interlink with Icarus, Page offers the agent a number of concessions based on what ending is being pursued, including money, power, Versalife itself, a spot on President Mead's cabinet or an entire continent (Europe).
- The Illuminati ending implies that Everett will work together with JC to restore the Illuminati to full power.
- We Gotta Stop Meeting Like This: Lampshaded during the conversation between JC and Simons, if the latter wasn't killed at the Ocean Lab.Simons: You take another step forward and here I am again, like your own reflection in a hall of mirrors.
JC: That makes me one ''ugly'' son of a bitch.
- "Where Are They Now?" Epilogue: Unlike the other two options, the Illuminati ending shows brief glimpses of what Alex, Carter, Reyes, and Tracer Tong are up to after the game's finale. The other two endings don't show the aftermath of J.C.'s final decision, largely because they're considerably more world-changing, while the Illuminati ending is much more of a return to the status quo.
- World Half Full: All three possible endings are improvements in comparison with the current situation: You can return power to the Illuminati (more benevolent conspiracy, which will allow you to distribute food and vaccine for the Grey Death), rule the world as an omniscient and benevolent AI (which lacks emotion and ambition) or take down communication, ensuring no one will be able to achieve global domination.
- You Can't Thwart Stage One: The blast hatch to Sector 4 won't open until the player speaks with Helios in the Aquinas Hub, at which point it will release the locks for the hatch.