The US Govt discontinued the SR71 Blackbird in the early 90's (or late 80's, can't remember when exactly). It was rumored around that time that they had discovered a craft to replace it that was far beyond the realms of what anyone had known about aviation to that date. It allegedly uses a power source that is extremely quiet, and has maneuverability unlike any other aircraft. Also, at some point afterwards, 3 of the SR71's were put back into service for several months at a time that coincides with 2 citizen's reports of seeing a strange craft crashing into the desert in Nevada. The craft was named by private investigators with the UAP (formerly known as UFO's) community the Aurora, after the name appeared on an Air Force line item in a budget report briefly. Shortly after it appeared on the budget, it was removed again just as mysteriously as the witnesses who saw the crash.
I can't personally confirm that info, I just saw it on the History Channel the other night on a program about the history of jet powered airplanes. But, to me it makes sense that the government would have something in place to replace the SR71's. They most assuredly haven't stopped using aircraft for surveillance.
Perhaps it was one of those craft that they saw. Or perhaps it was extraterrestrial. Personally, I can't believe we are the only life forms in the universe, and I also seriously doubt we are the most technologically advanced life forms in the universe.