X-51

As described in game, X-51 is a group of scientists, technicians, and ex-United States army soldiers, led by Dr. Gary Savage, who defected from Area 51 in 2051 after learning about the shadowy intentions of Majestic 12, the secret  organization led by the game's main antagonist, Bob Page.

When they walked out, they stole “everything smaller than a paper clip” according to X-51 member and scientist Carla Brown, and C-4'ed the large pieces of machinery at Area 51 that would make up the Universal Constructor needed for MJ-12's nefarious plans.

After their defection, they are said to have eluded UNATCO and the United States Army by posing as a research consortium and purchased Vandenberg Air Force Base, which had fallen into disrepair as a result of a catastrophic seismic  upheaval mentioned in the game's back-story only as the "SoCal Earthquake". They have had contact with the NSF, the Illuminati, and other resistance movements, however they are not coordinating fully with any  organization. Despite this, they are portrayed as well armed and their Vandenberg base as heavily fortified.

They are the only institution excluding MJ-12 who are said to possess a "Universal Constructor", a device with which they hope to find a cure for the plague known as the "Gray Death", a pandemic that has spread across the planet within the game.