The UFO field is literally chocked full with bizarre theories about "retroengineering" projects to build aircrafts based on alien technology or build advanced machines based on previously unheard of technology.

The UFO field is literally chocked full with bizarre theories about "retroengineering" projects to build aircrafts based on alien technology or build advanced machines based on previously unheard of technology.
Now, there’s little doubt that secret projects have been carried out and are still carried out to this day. For example the infamous "Aurora" high speed aircraft is more or less accepted as real. Many analysts believe it’s probably an high speed "unmanned surveillance platform": a supersonic drone fitted with state of the art recon equipment to use a simpler language.
This is by no mean a novel idea: the Americans experimented with the D21 high speed drone in the the ’60s but ended the program following a tragic accident in 1966 when the D21 drone pitched and destroyed the M21 "mothership" (an highly modified SR71/A12) killing the crew.

A good example of how secret projects work is Project Harvey, the program which led to the F117 Nighthawk stealth bomber.
In 1974 Project Harvey was launched to build an aircraft with the smallest possible Radar Cross Section (RCS). Interestingly Project Harvey wasn’t a "top secret" project: people just didn’t pay attention to it since it just seemed like a theoretical program.
When the Carter Administration took office in 1977 a defense undersecretary, William Perry was struck by how dramatic the results of radar tests on static models had been. The winning Lockheed design had such low RCS that it had to be cleaned regularly during the day since dirt and bird dropping increased its RCS by 50%. Perry immediately had Project Harvey decreed "top secret". Funding was dramatically increased and the project, when quoted in documents, was now simply called HAVE BLUE. Lockheed was ordered to build two flying demonstrators, simply called 1001 and 1002. These were put in anonymously looking crates, put in a cargo plane and shipped to Groom Lake in Nevada. The infamous Area-51 of UFO folklore.
1001 was painted in a highly disruptive desert camouflage scheme to confuse anyone who might get a glimpse of it. Test flight were surrounded by "extraordinary" security measures.
1001 didn’t last long since the test pilot had to put it down in a forced landing. He was seriously injuried but lived to tell the tale. 1001 was broken up with a bulldozer and buried in the desert.
1002 arrived a few months later. Security was tightened since the new aircraft was coated in a top secret Radar Absorbing Material (RAM). It was tested both against NATO and Soviet radar systems, whose presence at Groom Lake was yet another top secret matter (and the way they were obtained still is). Results were phenomenal. 1002 ended is a career during its 52nd flight, following an onboard fire. The pilot survived unscathed but 1002, just like its predecessor, was broken up and buried in the desert. So much for the fabled hangar full of flying saucers.
Lockheed was immediately ordered to build a scaled up version capable of combat named SENIOR TREND.
In 1980, following the Iranian Revolution and the embarassing Operation Desert One (a botched attempt to rescue US hostages in Iran) the Carter Admistration, desperate for consent, revealed the Air Force was working on a "stealth aircraft" . When Reagan took office in 1981 he personally ordered to make the whole program "black and invisible" a few days after moving into the White House.
The first five SENIOR TREND aircrafts, two test and three fully-fledged combat units, were given random designation numbers and were sent to Groom Lake using C5 heavylift cargo aircrafts.
A new unit, the 4450th Fighter Wing was established to fly the new aircrafts. They were housed in a new, top secret base build in the Tonopah Test Range.
Security was very tight from the start. The unit was given A7 attack aircrafts as a "blind" and to allow the pilots, all veterans with outstanding service records, to keep up flight hours. It was officially to be a "technical evaluation unit".
Pilots and crews were "officially" housed at Nellis AFB, where their families lived: each Monday afternoon they were taken to Tonopah with a jetliner after spending the weekend with their families. Flights only took place at night and accomodations were very austere. Each pilot was expected to fly a dozen SENIOR TREND missions plus six A7 flight a month. This was an extremely fatiguing schedule and was to have tragic consequences.
The hangars were opened only one hour after dark and closed up before sunrise. For the first year operations were restricted to the Nellis range and all routes were carefully plotted to avoid even sparsely populated areas. Some routes were not used if the Moon was over 50% full. All activities outside of the Nellis range were to be authorized Reagan himself. Call codes and transponder signals mimicked A7s.
Early details are murky and there are a number of reports of "weird looking" aircrafts being unloaded off C5 transports in both Europe (particularly Britain and Italy) and Japan: these may have been F117s but let’s not forget the Nighthawk wasn’t an easy aircraft to mantain and required dedicated facilities.
As said before fatigue was rapidly becoming a problem among pilots and, despite constant medical screening, the inevitable happened. On 11th July 1986 a family at a rest stop in the desert observed an unusual looking aircraft overhead in the early hours of the morning. They took pictures of it. Seconds later they heard a loud explosion and saw a fireball. Rescue teams were on the spot in minutes. Military Police confiscated the pictures but let the family off without further action since they weren’t breaking any law. I remember it clearly. The investigation turned out the pilot, a highly decorated and experienced major, simply flew the aircraft into the ground. He had probably fell asleep after an all night training exercise. The news was all over the world in days: I remember it clearly.
More accidents followed: another pilot was killed a year later when his F117 crashed into the desert. Cause was again "Controlled Flight Into Terrain": again the pilot probably fell asleep for a few seconds and crashed into the ground. A week later an A7 flown by a 4450th officer crashed into an hotel in Indianapolis, killing nine persons. The pilot ejected and survived unscathed. Again fatigue was to blame.
At this point somebody questioned if keeping the aircraft secret was still worth it. The originally planned 18 production aircrafts had grown to 59 (minus the two aforementioned losses) following extremely positive testing and the costs of keeping them at a top secret facility in the middle of nowhere was staggering.
The straw that broke the camel’s back was… an aircraft model.
F19 models had been on the market for years but were of such a dubious quality that nobody was seriously worried. In Fall 1987 Testors, a wll known model company, released the model of an hypothetical Soviet stealth plane called "MIG37B" featuring faceted surfaces, just like the F117. This was based on actual RCS studies carried out by Testors.
A year later the Pentagon released a press statement aknowledging the existance of the F117 Nighthawk stealth bomber, accompanied by a very ambiguous picture.
An actual F117 was shown to the press in 1990, just months before being redeployed to Saudi Arabia for Operation Desert Storm.

So what can we learn for this? Keeping a secret project secret isn’t that hard, provided you keep it relatively small. Many feel that the true reason the F117 was revealed to the press were the monumental costs associated wih keeping it a secret after production numbers had grown so much. There’s little doubt that if the program had stayed small it would have remained "black and invisible".