You might be interested in Annie Jacobsen's interview on the JRE. She argued that the 'flying saucers' were actually just an elaborate Soviet attempt at psychological warfare. I have no idea if it's true or not but it's entertaining at least, so I'll summarize it here.

The theory states that at the end of WWII, Stalin was feeling vulnerable because the US had the atomic bomb but the USSR did not. So he was interested in ways to try to destabilize the US and level the playing field.

So Stalin decided to have his engineers build some flying saucers and fly them into the continental US in order to freak people out. He also had some human cadavers surgically altered to look like aliens and them stuck them in the capsule for good measure.

By flying the saucers into the US mainland, the USSR hoped to put the US government in a bind. If the civilians who would inevitably find the craft were left to believe that it really was an alien ship, the prospect that 'we are not alone' would stir mass social unrest. On the other hand, if the govt identified the vessel as a Soviet aircraft, it would have to admit that the Russians were able to sneak into US airspace without the US military noticing, which would be a scandal in and of itself.

I think that story - as crazy as it is - is more plausible than actual aliens visiting Earth (though its not exactly a high bar). Stalin was certainly psycho enough to consider running such a harebrained scheme. It would also explain why the US govt would cover the whole thing up even if there were no aliens involved.

In any case, I am far more inclined to believe that any UFOs sighting is military-related than any kind of alien encounter.