The Story
Area 51 is a very high security US Air Force facility associated with Edwards Air Force Base. Located in Nevada, the area is highly restricted and all information about it is officially classified.
A secret branch of the US government uses this facility to house and study extraterrestrial artifacts. The most famous of which come from Roswell, New Mexico, where an alien flying saucer crashed in 1947. Several alien crew members were found at the crash site, and their bodies too are stored at the Area 51 facility.
The US Government does not admit that there was any flying saucer, or that it and other alien artifacts are stored at Area 51.
Facts
The first and last paragraphs above are true.
The second describes a conspiracy by the US government. That particular conspiracy is not true, but there really is a government conspiracy about Area 51, two in fact.
What crashed at Roswell in 1947 was actually a device for monitoring nuclear tests. The US military is naturally secretive about such things, and certainly didn't want anyone searching for lost equipment at the site. So, when knowledge of the crash became public, they held a press conference where they stated that it was simply a weather balloon that had come down near Roswell. This minor government conspiracy held up well, and the public accepted it for 30 years.
In the 1970s, UFO researchers looked into the incident and (correctly) decided that there was a government cover-up of what had actually crashed. Using the Freedom Of Information Act, they were able to find evidence to support the existence of this conspiracy. But being UFO researchers, they of course concluded that it was a conspiracy to hide an extraterrestrial space craft and its alien occupants. They wrote books about the matter, and soon so did many other writers that wanted to cash in on this now popular topic.
When the government and military denied that a flying saucer had crashed, and denied that it had been taken to Area 51, they were accused of being part of a conspiracy to suppress knowledge of alien contact.
This conspiracy theory is complete nonsense, but that doesn't mean that the government isn't conspiring about this crash and Area 51.
Why
The US government and military are conspiring about the Roswell crash and Area 51, but not in the way most people think.
Instead, by denying that the Roswell incident involved a flying saucer, denying that they recovered alien bodies from the side, and keeping Area 51 an extremely secret and heavily guarded area, they are in fact encouraging this conspiracy theory. And they are doing it intensionally.
Area 51 is actually used for testing new military aircraft and similar devices, and occasionally the public might see some military secret. As long as Area 51 is continually watched and studied by flying saucer nuts, the sane part of the world will never believe anything they report. Russia, China, and other countries will not be able to filter out the small number of true sightings from the large number of fantastic reports that the UFO enthusiasts (and local tourism industry) generate. And that is good for protecting military secrets.