The Antimatter Reactors are never given much in-game explanation, but if the musings of the sole mechanic near the reactors is to be believed, they were reverse-engineered from an alien crash site in Roswell. However, based on other facts, it is likely the rumors of alien involvement are false information meant to conceal their true nature and discredit anyone who defects from MJ12 and attempts to expose their activities. The mechanic mentions that the reactors are unstable, and, despite their extreme energy output, they are only used for tests.
As the name implies, theoretically Antimatter Reactors would use antimatter reactions to generate power. The reactors would combine identical particles of opposing charge, creating a violent reaction where the two particles are "annihilated" and a massive energy output is released. Thus, these reactors are capable of near-infinite, renewable energy with a higher efficiency than any other current power source, but at the same time are capable of violent explosions far more powerful than nuclear devices.
At the end of the game, Tracer Tong will try to convince the player to cut off the coolant and failsafes to the reactors, and then activate them, causing a meltdown that destroys Area 51, the hub of all the world's communication systems, making a "New Dark Age". The player must choose between this, the Helios Ending, and the Illuminati ending. The coolant is located in Sector 4, near the bottom floor of the Nanotech Infusion Chamber. The failsafes are located on the side of both reactors, though the pits are filled with hazardous radioactive waste, and some Grays.
- Once the player stops the failsafes and coolant to the Reactors, the mechanic in the control room will realize what the player is attempting to do and shoot at them with a 10mm pistol.
- The coolant reservoir begins in a tunnel under Page's Infusion chamber, then moves west for several hundred meters, where it moves up to the reactors. If the player swims through this pipe to the end, they will reach 2 deep pits surrounded by chain link fences. If they dive to the bottom of the pit with a soldier floating in it, they can find a LAW, but this is difficult to do without the Swimming skill, a rebreather, or aqualung.