When it comes to mysteries, area 51 takes the cake for most people. It has been one of the most well known subjects of conspiracy for decades and will be for decades to come. Some people say they store alien aircraft or even alien bodies are there. What lit the fire for this conspiracy was "the Roswellincident".
On the 8th of July 1947 an aircraft of unknown origin crashed near Roswell. The army is said to have taken 3 bodies from the crash site, ruling out the possibility of it being an weather balloon, which was the first explaination for the aircraft by the government.
While that incident happened decades ago, many people still believe area 51 houses an alien aircraft and alien remains. Area 51 states their job is of importance to (inter)national security, which also causes people to think Area 51 might be working on reverse engeneering alien aircraft. It is a nice story, but I personally don't really get the comotion around Area 51. I took it upon myself to find a more reasonable explaination for the secrecy surrounding the base.
Area 51 has always been in use as a base for developing aircraft and militairy equipment. Primairily weaponry. This already concludes my explaination. The reason why the events that take place within Area 51 are Top Secret is just simply that no one may find out what happens there. If plans for a new aircraft/weapon fall in the hands of oposing parties, not only Area 51 but also America as a country would be in trouble. They might be holding an alien aircraft and a few alien bodies yes, but besides that being unlikely to me that also doesn't look like the reason as to why Area 51 is operating in secret. When developing state-of-the-art technology, you don't want other to know and that alone as a reason is enough for a militairy base like Area 51 to be silent about what they do. To me, it wouldn't seem like a big deal if they are holding aliens and the alien technology from a simple aircraft housing 3 crewmembers might not be all that overwhelming.
(The many "UFO" sightings around the base indicate test-flights of unknown aircraft. UFO is the name for an unidentified flying object (so UFO for short) and does not indicate the aircraft being of alien origins.)