Although it was originally owned by the military, it was condemned after the SoCal earthquake left most of the underground sections of the base flooded, collapsed or leaking toxic chemicals and radiation. In addition, the security systems had gone rogue, and several Chiang M2s now patrol the underground, attacking anything that moves. Following the cataclysmic Californian earthquakes of 2030, the entire facility was evacuated, and 21 years later, escaped scientists from Area 51 settled here and called themselves X-51. These scientists, led by Gary Savage, have nearly built a complete Universal Constructor, only lacking a containment unit.
In 2052, Majestic 12, sensing the possibility of X-51 curing the Gray Death with their Universal Constructor, invades the facility and captures many of the base's personnel. Those that do escape lock themselves in the Control Center of the main building and Communications center 01, a small building in the courtyard. JC Denton is sent here to aid X-51 and drive off MJ12. Included in MJ12's forces are 2 Bravo-3 Peacebringers and 2 Delta-2 Peacebringers, located in the courtyard.
It was said than a unit of NSF troops should arrive to Vanderberg soon to protect the base, but they haven't arrived when JC departed.
The base has 3 floors, a roof, a courtyard, and an extensive system of underground tunnels under the complex.
- Roof – JC lands here. Location of one X-51 scientist, and two MJ12 Troopers who Jock guns down on landing. There is a large skylight JC can break to fall down to the first floor's roof, and if he is properly augmented, he can survive the jump down to the ground. On the far edge, unaccessable from the point JC is dropped off at, several LAWs can be found, which are useful for destroying the bots in the courtyard.
- 3rd Floor – An industrial area, with an elevator on one end. The rooms are cramped and well guarded, but contain many supply crates.
- 2nd floor – Location of a small waiting room and a staircase leading downstairs. There are two heavy blast doors leading to the Control center, where most of the scientists and MILNET servers are.
- 1st floor – Location of the lobby, a flooded laboratory, and a locked supply closet. Behind a vent in the lobby, the player can climb up to the roof, where LAWs can be found.
- Courtyard – Location of Com centers 01 and 02, though Center 02 is unaccessible. Center 01 houses a few mechanics and scientists, and a trap door in the closet leads to the underground tunnels. Many bots patrol the courtyard, and all of them must be destroyed or deactivated to progress in the game. At the far end of the courtyard is a road leading to an old security checkpoint in front of the facility. Jock will land his helicopter here.
- Underground tunnels – Although flooded and collapsed, the tunnels must be traversed to find the key to the control room. The radiation can be easily avoided, and the turrets can be disabled through hacking the security terminals, but care should be taken in eliminating the bots. If the player has not invested any points swimming skill, it is nearly necessary to at least upgrade it to Trained, or use a rebreather.