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 sees and tries to go public with it. The mechanic mentions that the reactors are unstable, and, despite their extreme energy output, they are only used for tests.