History

DC

"They say there are genetic monsters in the basements, aliens conspiring with corrupt officials, and more doomsday weapons to the square mile than anywhere else on Earth."
--Batman

In DC, Area 51 is a super secret government facility in Nevada.

Marvel

In Marvel, at some point the site was closed and a 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 the Gamma Corps as headquarters, thought it was eventually bought by Tony Stark, who used it to store the Reality Gem.

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.

Dynamite Entertainment

In Dynamite Entertainment, not only is Area 51 the location of countless aliens, it is also where the original American Crusader was housed after World War II. He was subjected to cloning for the next sixty plus years.

It was not until Black Terror was released from the Urn of Pandora that he was eventually rescued/killed as his person was molded with the Colonel who was in charge of the facility Marcus Chamberlain. This is the event that led Marcus Chamberlain to become the next American Crusader.