Area 51 is a secret USAF base located in Groom Lake, Nevada. It is believed that in 1947 what became known as the Roswell UFO Incident a ship containing Grey Extraterrestrials, crashed in Roswell, New Mexico. These alien were said to have been taken to Area 51 for study.
At some point the site was closed and new facility dubbed "Area 52" in Utah was created to contain "mysteries of America," including superhuman-related technology. The abandoned Area 51 was then used by General John Ryker, and later the Gamma Corps, as headquarters.
At some point in time, Area 51 was the site where the In-Betweener was held captive before being freed by Miss America on Barnell Bohusk's and Angel Salvadore's intel, and the two of them were targeted in the desert next by Braak'nhüd.
In Earth-11052, Nick Fury sent the X-Men to Nevada to rescue mutants whom were being held captive in Area 51. During the operation, Cyclops intentionally left Mystique behind, but she later escaped.