New West Coast
The helicopter arrives just outside an abandoned gas station in California. With the help of a pair of homeless people, JC obtains a key and accesses a sewage tunnel leading to the station.
Once there, he dispatches several MJ12 troops and rescues Tiffany, who reveals that she didn't get the Containment Shield schematics necessary to finish the Constructor. Jock drops her off back at Vandenberg, and he and JC continue on to the Sub Base where Tiffany was caught.
JC discovers that the base is filled with heavy security bots, MJ12 snipers and troops upon his arrival. He sneaks into the upper labs and discovers several scientists who have been forced to work by MJ12, and who give JC information that he would need to go to an nearby Ocean Lab to retrieve the schematics. JC continues through the base, and eventually boards a submersible that takes him to the underwater ocean lab.
Upon arriving, JC discovers that a rogue scientist named Ridley sabotaged the lab by partially flooding it. Wild greasels are everywhere, all of the staff have been massacred and the lab's defenses are running rampant.
JC continues through the lab and an unfinished mining area to the UC repair area, where dead engineers are lying in the hallways and a spider bot patrols the area. JC eventually makes it to a computer room and retrieves the schematics from the UC chamber. Savage calls and tells him he's getting what he needs.
On his way back, Page appears on holocomm and goads JC's alleged success. He says that even if Savage and the scientists are able to synthesize a cure, he will just create a new virus, and insinuates that he is planning to launch a missile at Vandenberg. JC heads back to a nearby elevator, but Savage warns that another submersible has already docked at the base. Simons radios JC and insults him for being a "flawed prototype".
In the mining area, Simons confronts JC and says that he's going to terminate the agent himself. JC runs past him and escapes, and dispatches two MJ12 frogmen before using the submersible to return to the Sub Base.
Once there, he meets with Savage on the base's helipad. Savage thanks him for rescuing his daughter and says that they will have the first batch of the vaccine ready by nightfall. He also gives JC the location of the Missile Silo where Page is planning to fire off a rocket that will destroy Vandenberg.
With little time left on the clock, Jock lands near the silo and tells JC to hurry. The agent finds many troops, dogs and a security bot patrolling the base, and dispatches them all while heading to an access door. Savage gives him a code to access the launch control station, and JC finds a scared scientist who was locked up by MJ12 and tells him that the troops massacred the scientists and took it over recently.
JC finds the launch controls and reprograms it to hit Page's hideout, Area 51, instead. Page radios him once more to gloat and say that he is still in control of the missile, and Savage asks JC to find and kill Page's lieutenant who is guarding the missile.
Continuing through the silo, JC avoids a trap and dispatches more soldiers on his way to the lieutenant, Howard Strong. After JC takes out Strong, Savage congratulates him on his work and JC exits the silo.
Jock is waiting up above and says that they'll get a hero's welcome when they get back to Vandenberg. JC tells him that they're going to Area 51 instead, and that he's going after Bob Page alone.
The helicopter lifts off as the missile is fired out of the silo...
- All There in the Manual: Supplemental material (the Deus Ex Bible) explains that Howard Strong has a case of Ambition Is Evil, and was initially a low-ranking soldier who worked his way into Page's good graces, and was given a platoon of soldiers and the job of holding the Missile Silo.
- Apocalyptic Log: Various datapads can be found throughout the ocean lab, which detail Ridley's sabotage and eventual death.
- Calling Your Attacks: Page essentially informs JC that he's going to fire a missile at Vandenberg, expecting that they're not going to do anything. On the contrary, Page's threat allows JC to intervene and stop the launch before redirecting it at Area 51.
- Contrived Coincidence: If Sandra Renton fled from the 'Ton Hotel in the "UNATCO Transmitter" mission (either as a result of her father dying or said father killing Jojo himself), she winds up broke and homeless... right beside the gas station where Tiffany Savage is being held. Bear in mind, we last saw her in NYC, the opposite side of the country.
- Dare to Be Badass: JC chooses to assault Area 51 by himself in the wake of the missile detonation in order to catch Bob Page off-guard, even though Jock says they should wait for backup.
- Developer's Foresight:
- One of the scientists in the Ocean Lab will acknowledge the player's use of swimming through the Karkian tank and exiting next to her while entering for the first time, even though this requires the player to either deliberately ignore the scientist by the tank area, or enter the base from the docks (and swimming over to a ladder leading up into the offshore platform, instead of accessing the spiral stairs) and working their way backwards through it. Taking this option results in a What the Hell, Hero? response from the scientist, who complains that JC "can't screw anything up more than you already have" and gives him the code to the tank anyway.
- If you choose to redirect the missile and kill Howard Strong in the silo before doubling back all the way to the washroom to rescue the imprisoned scientist, JC and the scientist will have an alternate conversation where he tells the latter about what's happened and promises to stop Page once and for all.
- Dynamic Entry: The player can pull this by leaping onto Howard Strong from a higher level of the silo, which kills him instantly and ends the mission.
- Elaborate Underground Base: The Ocean Lab, which has an entire underground wing dedicated to production of Ambrosia and Gray Death and some computer banks. This may have an explanation, as parts of the level (specifically, the outer [underwater] area of the Ocean Lab) were repurposed from the cut "moonbase" level.
- Giant (Robot) Spider: The Chiang M5 mecha-spider (a larger variant of the smaller MJ12 spider enemies) can be seen guarding the elevator to the Universal Constructor.
- Goomba Stomp: The most bizarre method of killing Howard Strong.
- Ignored Expert: Played for Laughs. The surviving scientist in the Silo gives his explanation of what he thinks is a conspiracy, which is actually the exact threat JC has been fighting against for most of the game. When he remarks that he doesn't want JC to think he's crazy, the agent responds, "I never called you crazy."
- Jump Scare: The Karkian hiding in the crew module in the Ocean Lab's construction zone, who's situated right behind a wall and leaps at you as soon as you enter to get a needed key to progress.
- Late to the Tragedy:
- The player arrives at the Ocean Lab just after a scientist sabotaged the base and killed all of the personnel.
- The same thing happens at the Missile Silo, where JC arrives just after MJ12 has killed nearly all of the scientists and seized control of the facility.
- The Mole: Several of the scientists at the Sub Base, despite being directly managed by MJ12, are still loyal to Savage, and ask JC to give him their regards out of earshot of the troops.
- Sequence Breaking:
- It's possible to skip the fight with Simons completely by lacing the front of the bulldozer in the mining area with a LAM or two, which blows him up before you can even open the door to face him.
- Due to a quirk with the way certain missile weapons are designed, it's possible to start the Silo mission, run to the exit hatch above the silo and (if a weapon like the GEP Gun or LAW anti-tank weapon is positioned a certain way) can be fired through the hatch and downwards, killing Howard Strong and ending the mission in approximately a minute or less.
- Series Continuity Error: During the trek through the Ocean Lab, a Man in Black can be found floating dead in the water next to the elevator leading up to the UC — the only instance of an MIB found in this way, as the characters are typically programmed to explode if they are killed by any means.
- Skippable Boss: The fight against Simons can be skipped if the player chooses to sneak past him (or runs past him without even realizing he was in the room).
- Upgrade vs. Prototype Fight: The fight against Simons, unless the player sneaks past him.Simons: I am the more advanced model, Denton. It's time for you to retire.
- Villain Ball:
- In the Ocean Lab, Page specifically calls JC to goad the latter about his plan to destroy Vandenberg, thus giving the agent and Gary Savage the heads-up and allowing them to act accordingly.
- Discussed and lampshaded. Enemy Chatter in the Silo level includes several soldiers talking about the current operation over drinks. They wonder why Page and Simons would do something stupid such as putting a known opportunist (and loose cannon) like Howard Strong in charge of a sensitive military operation, and begin to question the effectiveness of Page's coup.
- Due to the way his boss fight area is designed (standing on a raised platform above the lowest level of the Missile Silo), Strong is just as likely to self-gib himself with a LAM as he is to deal fatal damage to JC.
- You Can't Go Home Again: Discussed — JC tells Sandra (if she fled New York) that she could go back if she felt like it. Sandra says she still wants to stick with her plan to walk to Eugene, California, despite missing her friends and her normal life. (Then again, considering Hell's Kitchen is only getting worse due to a combination of Emergency Authority and the riots, it's likely she couldn't get back even if she wanted to.)
- You Can't Thwart Stage One: Once JC hits the override switch to redirect the missile, Savage momentarily celebrates by telling Page "it's going to be a sunny day at Area 51"... before Page intercedes and tells him that "premature celebration" was his Fatal Flaw, and that he's prepared for that scenario. What follows is JC having to assault the silo itself to stop Howard Strong from manually controlling the launch.