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 let the Illuminati run the world like the old days.
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.
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 tells the AI to do it, and 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 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 and they discuss how transportation and society are getting back to normal like the old days. When JC questions what they've accomplished, Morgan explains that together, they will lead humanity...
- 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 Vanity: 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.
- 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.
- 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 Is 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.
- 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. 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 asking 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Snark-to-Snark Combat: JC's conversation with Page in Sector 4.
- 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.
- World Half Full: All three possible endings are improvements in comparison with current situation: You can return power to 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.