Some believe the legend of aliens is a cover story to hide the fact
that the USA in the 1950s and 60s developed cybernetic organisms -
humans that were medically engineered to survive in space without
benefit of a spacesuit.  Such cyborgs would bear a distant resemblance
to human beings, and would have an interest in human reproductive
systems to maintain themselves.

http://en.wikipedia.org/wiki/Cyborg
http://en.wikipedia.org/wiki/Manfred_Clynes

These same people also believe that the USA made much more progress in
the field of nuclear powered aircraft than has been made public -
again the legends of UFOs are a handy cover for these craft

http://en.wikipedia.org/wiki/Nuclear_aircraft
http://en.wikipedia.org/wiki/Project_Pluto
http://en.wikipedia.org/wiki/NERVA

These programs begun in the 1950s, were canceled by LBJ in November
1963.

Some believe these may have gone underground and not abandoned as is
publicly thought.

A nuclear powered aircraft could hover for long periods of times on
nuclear powered jets.

http://en.wikipedia.org/wiki/Avro_Canada#Experimental_programs

Nuclear powered rockets could fly to the moon and back in a single
stage, in hours, and fly throughout the inner solar system in days

http://en.wikipedia.org/wiki/Antimatter_catalyzed_nuclear_pulse_propulsion

Flight systems that use cyborgs would be extremely lightweight,
compact and very capable.

Such flight systems and personnel could establish bases on the moon
and mars for the world's leadership if life became untenable on Earth
for any reason.

We have done this before.  From 1959 through 1961 the USA secretly
built a nuclear bunker for Congress.  The shelter was closed in 1995.
What replaced it?

Instead of jets spiriting away leaders to bunkers in the hillsides,
what about nuclear spaceships piloted by cyborgs taking our leaders to
outposts on Mars or the Moon?  Outposts and flight systems that had to
be maintained by a population of cyborgs.

Where do we get cyborgs?  Assuming we know how to make them and have
need of them?

Entire towns have disappeared in the past.  What happened to them?
Some legends have suggested UFOs and aliens.  A much more prosaic
answer to this question is possible - the ultimate in slavery.  Pick
up humans of little consequence here, and rebuild them into cyborgs.

We have the technology, and quite frankly, this makes more sense than
aliens.