Reporters and activists have unearthed many military secrets, and some have been disclosed officially over time. But what military secrets have remained secret?

Who wrote the Stuxnet and Flame malware that delayed Iran's nuclear enrichment program? It is unofficially acknowledged that it was U.S. intelligence and money, combined with Israeli brains and laws.

How did someone—it's not hard to guess who—bomb Syrian and Sudanese weapons facilities and leave barely a fingerprint behind? Doubtless it was the Israelis, showing what you can do with non-stealthy aircraft, new weapons, advanced electronics, first-rate training, standoff sensors and airborne command and control.

Did the Iranians shoot down an RQ-170 in November 2011? No, it crashed without outside assistance and was put on display largely intact by the Iranians. U.S. Air Force acquisition officials say that would not have happened if they had run the program, instead of Lockheed Martin's special projects operation. They say safety precautions and self-destruct capabilities were sloppy or missing.

Where are all the Russian weapons that scared everyone during the Cold War? Since the Soviet Union broke up, nobody knows for sure, not even the Russians. Can we see missile-carrying submarines under the water? Sometimes water turbulence can be detected by aircraft or even satellite sensors, so in theory, yes.

Can the military and national intelligence agencies, even your corporate bosses, read your innermost thoughts? Yes, but only if you are dumb enough to email them or write them somewhere on the Internet.

Is there any way to protect yourself from cyberexploitation? Maybe, with some good offensive tools. But the government has spent years not making decisions on how to prepare for offensive cyberoperations. (Lawmakers apparently have been too busy reading other people's email.) The White House is once again leading the charge to make a little progress in codifying cyber-rules, weapons, targets and jurisdictions. Congress stalls legislation, citing privacy concerns. A citizen might well question what privacy is left if the FBI, CIA, National Security Agency and the full-court cyberhacker team from around the world are picking through his or her files.

What was really going on in Groom Lake, popularly known as Area 51, and the Tonopah Test Range (TTR)—part of the restricted Nevada test ranges northwest of Las Vegas—in the heady 1980s and 1990s, replete with rumors of aliens and recovered flying saucers?

TTR was home to flying objects that would not have raised an eyebrow—if you lived in East Germany. What started with some “borrowed” MiG-21s and MiG-17s to develop tactics for use in Vietnam grew into the squadron-sized Constant Peg program operating MiG-21s and MiG-23s. That “Red Eagle” program in turn provided cover for the more tightly classified Red Hat technical exploitation project. Some foreign weapons used in those programs can be seen today at the threat museum (also known as the Petting Zoo) at Nellis AFB, Nev.

Groom Lake and TTR expanded with the defense boom during the Reagan administration. Chartered airliners ferried work crews and pilots to the site every day. New hangars and runways were built. As UAVs started making their appearance, some were designed for stealth, which meant that they, too, were “sight sensitive.” Like all but two of the aircraft tested there since the 1980s, they remain secret.

Also tested at Groom and TTR were the Suter network exploitation programs. Experimenters set up an integrated air defense system (IADS) and hit it with an EC-130 Compass Call electronic attack aircraft and an RC-135 Rivet Joint signals intelligence platform. The Compass Call transmitted a data beam, packed with algorithms, directly into one of the IADS's antennas. Like a malware package, it allowed the invaders to see what the enemy sensors saw, and to control their movement—even to the point of directing radars away from friendly aircraft. The malware was also designed to spread across the IADS network and infect dispersed sensors and missile launchers.

Secret programs are rigidly compartmentalized—Groom Lake's windowless hangars and offices went into lock-down during flight tests. The fighter pilot network appears to have been the best way to figure out how to start, fund and field new programs—although a U.S. Air Force pilot told Defense Technology Edition Chief Editor Bill Sweetman at a recent lecture on Constant Peg: “I used to fly with all these guys, and I never had a clue they had done this.”

Repeated but so far unexplained nighttime sightings have included huge, silent “flying triangles” that sounded rather like the extraterrestrial mothership in the movie “Close Encounters of the Third Kind,” blotting out the stars. Big lighter-than-air vehicles or travelers' tales?

Airliner pilots passing near the Nevada test ranges have reported seeing things that looked and behaved strangely. (In the 1950s and 1960s, the Air Force and CIA collaborated to discredit pilots' real U-2 and A-12 sightings by lumping them together with UFO reports.) Similar accounts appeared out of the Middle East during Operation Desert Storm, the first Iraq war. U.S. pilots interviewed by Aviation Week said they were flying at around 40,000 ft. and saw contrails of aircraft flying far above them. The SR-71s were long retired. There are still mysteries to solve.