Jock's helicopter lands on the roof of the Vandenberg facility, scaring away two soldiers who were trying to attack a scientist. She thanks JC and tells him that the facility was invaded by MJ12 in a pre-emptive strike to prevent them from completing their own Universal Constructor.
Jock radios and tells him that before he can access the area where the surviving military personnel and scientists are holed up, he will have to take out four security bots patrolling the front of the building. He also says that he has to leave for a bit to pick up Tong, who has arrived in the U.S. but is stranded with no means of transportation.
JC heads through the building and takes out multiple troops. Everett radios him to say that Daedalus is being attacked by another AI, Icarus, and that JC will have to uplink a program called Milnet once he gets to the locked-down control room. Everett reasons that doing so will save Daedalus and destroy Icarus.
The bots are destroyed by JC, and he gains access to an communications room outside the base. A handful of staff tell him that to access the control room, he will have to go through the maintenance tunnels underneath the base and retrieve a key from the scientist who had it. JC does so and finds the key, encountering greasels and pockets of spilled nuclear waste on his way.
JC emerges back in the base and uses the key to access the control room. Inside, he finds... Sam Carter, who tells him that he was kicked out of UNATCO along with all of the long-running staff, and that they were all replaced with soldiers loyal to Simons. Carter tells him that he came to Vandenberg to help out and that he should go talk to the head scientist, Gary Savage.
Savage greets JC and says that they have a nearly-complete Universal Constructor, save for one component which his daughter is bringing back to the base. Savage asks him to uplink Milnet, which is located in an adjacent (and electricity-filled) room. When JC does so, Daedalus and Icarus unexpectedly merge into another being called Helios, and Bob Page calls to gloat that activating Milnet has fit right into his plans.
JC goes back to the control room and finds out that although the Constructor is now operational, connecting Milnet has resulted in Page using Icarus to overtake Daedalus and create a new AI. Page also appears to the group on holocomm and announces that he has kidnapped Tiffany, and orders Savage to bring him a critical part of the Constructor in return for her release.
After the communication ends, JC says not to give in, and that he will mount a rescue mission to get Tiffany back. Both Savage and Carter think he's doing the right thing, and he exits the base. Jock appears at the bottom of a hill located near the base and reveals that he has brought Tong, who has been afflicted with the Grey Death.
Tong says that he's there for personal reasons and wants a cure, and JC says that he will get the required components for the Constructor and have a cure soon.
Tong walks back to the base, while JC and Jock head towards the location where Tiffany is held...
- The Bus Came Back: Carter reappears after he said he wanted UNATCO back on track, and reveals that he was booted from the organization in the interim.
- Classical Mythology: Daedalus and Icarus are influenced by Greek mythology, via the well-known story of Icarus attempting to fly too close to the sun after Daedalus builds him a set of feather-and-wax wings.
- Developer's Foresight:
- If you choose to run away from Stephanie Maxwell (who begins talking to you within two seconds of beginning the level) and go to another part of the roof (or just go into the building), Jock calls and relays everything that Stephanie would have said, up to and including a keycode that he had no way of knowing himself. Likewise, Stephanie's dialogue changes after this.
- Stephanie has additional dialogue if you go back up to the roof and talk to her after destroying the four sentry bots, despite there being no other reason to visit.
- Game-Breaking Bug: In certain early versions of the game, Page would never appear after asking JC and Savage to step over to the holocomm, thus breaking the player's game for good. There was no way to fix this without beginning a new game, although later patches removed the problem.
- Hostage for MacGuffin: Bob Page tries this, holding Tiffany Savage and demanding components for his own Universal Constructor.
- Just in Time: Jock pulls this when he arrives just before a researcher hiding on top of the building is gunned down by snipers. Later, the player can pull this by rescuing several scientists before they're attacked by MJ12 troops.
- Late to the Tragedy: JC and Jock show up to Vandenberg after the place has been sieged, with the tunnels underneath the complex filled with dangerous test specimens running loose, radiation that has leaked, and an Apocalyptic Log written by one of the researchers who ventured into them trying to find a key to the control room.
- The Lost Lenore: The researchers inside the control room can tell JC that Gary's wife was assassinated prior to the events of the game, which is driving his confusion and shocked reaction when Tiffany is kidnapped by the exact same group, MJ12.
- Monumental Damage: Travelling to the edge of the main map (the bottom of the path leading down to the guard station outside the base) reveals some of the damage caused by the "SoCal earthquake=]" that destroyed a major portion of the West Coast in the United States. Based on information found in other titles (including a draft email in the Picus Corporate Vault in Deus Ex: Mankind Divided that is suggested to be foreshadowing the implementation of an earthquake, as well as comments from Samizdat members) and a conversation between Debeers and Everett in Deus Ex: Icarus Effect, it's heavily implied that the Illuminati initiated the earthquake by utilizing a faultline.
- Nice Job Breaking It, Hero: Everett's quest to merge Daedalus and Icarus backfires on him, as they become a single, more-powerful unit that is under Page's control.
- Sequence Breaking: The easiest way to end the lockdown is to simply chuck a scramble grenade off Vandenberg's roof (which can be done seconds after starting the level), which causes a heavy security bot to kill the two smaller sentries and the MJ12 commandoes outside the comm building, and skips a large part of the opening section.
- Sinister Surveillance: The AQUINAS Protocol, which Page uses to listen in on JC and Everett's plans.
- Xanatos Gambit: Page's plan was to use Icarus to goad Everett (and JC) into merging the two AI's, which results in Helios being created and Page revealing that he had been keeping tabs on JC the whole time.