I just wrapped up Skunkworks and put the book down pretty impressed at what the DoD and Lockheed were able to keep secret. The author described Skunkworks' miss

I just wrapped up Skunkworks and put the book down pretty impressed at what the DoD and Lockheed were able to keep secret. The author described Skunkworks' mission "again and again" as creating aircraft that were technologically unbelievable to America's enemies, so they would have no means to even reckon with a defense. The USSR spent hundreds of billions of rubles on an impenetrable anti-air defense network, Lockheed built a plane that could fly right through it and drop a bomb through a Kremlin chimney, and everyone kept it a secret for years. The author also repeatedly alluded to projects from throughout his career that remained classified at the time, one of these was the F-22. My takeaway there is more that it's believable pilots have sighted unidentifiable aircraft exhibiting technologically implausible behavior because those craft are classified projects, rather than because they're extraterrestrial craft, but I don't think it's so plainly unbelievable that the government can't keep secret projects under wraps. The stealth modified helicopters used in the Bin Laden raid come to mind, and really, those are pretty boring as far as "top secret technology" goes, and were apparently in pretty regular use already.