It seems the most satisfying explanation to many people regarding Extraterrestrial Biological Entities is also the most common. One day, for reasons we cannot fully understand for sure, creatures piled into a saucer and set out exploring the universe. When they found a blue water covered planet named Earth, they decided to stay.
Traditional accounts of alien visitation say they began with a study of human biology and physiology, but eventually ended with the extraction of reproductive material and the creation of a third hybrid species. How would this have played out from the perspective of an objective viewer capable of spotting the aliens? And what are the possibilities for government involvement?
First, it seems the most obvious aspect must be addressed first. If the government were involved directly in some sort of arrangement between humans and the visitors, it would require serious compartmentalization of government organizations so each could work independently without leaking information, very similar to the compartmentalization that has become more pronounced in the past fifty years. Very few people, including those working at places such as Area 51 would actually have any conception that there was such a thing as aliens.
Likewise, a cover-up would likely be a matter of real national security. There are scenarios that are very easy to think of that would be directly related to the security of nations involved as their revelation would directly or indirectly damage or even dissolve their sovereignty. Signing a pact with an alien nation may have been considered necessary for the survival of the human race, but would doing so also have been an act of treason? And the visitors would likely not want their actions to be detected by the general populace, but why? Obviously this secrecy would work to serve some goal, and therefore that goal could be blocked by our limited abilities if it was known.
Given the scenario of alien visitors in the form of biological entities, the most obvious question is, are they friendly? Are they serving our goals even while serving their own? For that matter, if humans are interacting or communicating with these creatures are they friendly or are they merely playing games with humanity as a resource rather than the goal? There are circumstances where the visitors could be both friendly and secretive about their presence. It seems also that any serious inquiry into the matter is blocked by unforeseen circumstances even while tabloid-esque coverage of the topic is almost encouraged. And it seems to feed some sort of need within the UFO community.
Furthermore, the intervention of alien UFOs on nuclear missile silos is at once heartening and troubling. Wouldn’t it be the most incredible conspiracy of all time if alien visitors had come down to our planet and in an effort to help us through the nuclear uncertainty of the 20th and 21st centuries, had disabled the world’s nuclear arsenal in a way that led everyone to think they still had the ability to destroy the world without actually damaging the experiment. Picture it: nuclear war is declared by several superpowers and humanity waits in solemn silence for the world to end, only when the bombs drop they find by some miracle not a single one works with no explanation.