It's an Interrogation Center for Captured Aliens
In the imaginations of conspiracy theorists, one of Area 51's functions is to serve as the equivalent of the prison for accused terrorists at Guantanamo Bay. The difference is that the detainees are extraterrestrials, and they don't have to wear orange jumpsuits or listen to loud heavy-metal rock when they're trying to sleep. This thesis is burnished by another of self-described Area 51 scientist Bob Lazar's revelations. He has recalled that while being guided down a hallway at S-4, he momentarily glanced through a small window and caught a glimpse of a small, gray extraterrestrial standing between two men dressed in white coats. Before he could get a better look, he was pushed by a guard who told him to stop looking and keep moving [source: Jacobsen].
Another self-styled whistleblower, "Victor," who also claimed to have worked at Area 51, said in a 1997 radio interview that he had witnessed an alien interrogation, and even provided a grainy video which supposedly shows a human officer trying to communicate telepathically with an diminutive extraterrestrial pilot who'd been shot down by the U.S. military [source: UFO Casebook].