In 2009, authorities in the west African country of Mali discovered a 1978 Boeing 727 that had recently burned in an isolated region of the country’s northern desert. The aircraft landed there after taking off from Venezuela, intelligence sources later reported, loaded with nine tons of cocaine. According to the U.S. Drug Enforcement Administration, the wholesale value of the cargo was $225 million. Law enforcement officers believe the cocaine was taken north from Mali and eventually smuggled into Europe.

Just two years earlier, that 727 had been the property of Finova Capital, a finance company in Scottsdale, Arizona. Finova sold it in 2007 to a Spain-based subsidiary of West African Aviation. In the two years between its sale and its destruction, the aircraft was owned by three entities in four countries and assigned three different registrations. Its last airworthiness certificate, granted by the Saudi Arabian General Authority of Civil Aviation, had expired. Investigators determined that the airplane had been torched by the crew, but no crew member has been found.

The “Mali drugplane,” as the 727 became known, is a “ghost plane”: a term United Nations investigators use for aircraft with false registration numbers, lapsed certificates of airworthiness, or missing or incorrect manufacturing numbers, and usually with long, byzantine histories of ownership or leasing—in other words, airplanes that are very difficult or impossible to trace. One day an aircraft is flying for a charter service, delivering humanitarian relief cargo for an NGO or hauling freight to a mine; the next day it is gone, never to be seen again, or, like the Mali drugplane, reemerging in some nefarious operation.

I became intrigued (some of my friends say “obsessed”) with the search for a ghost plane in 2010, when I wrote about Boeing 727 N844AA, which took off one day from Luanda, Angola, and has not been seen since (see “The 727 That Vanished,” Sept. 2010). When I started research for the article, I thought the case of N844AA was extraordinary, perhaps unique. Since then, I’ve learned that there are hundreds of ghost planes, most of them spirited out of Russia after the 1991 dissolution of the Soviet Union. What is more shocking—and potentially more dangerous—is that the vanished airplanes include almost 50 large U.S. transports: 11 Boeing 737s and 26 707s and 727s; two Douglas DC‑8s and two DC-9s; two Lockheed L100s (the civilian variant of the C-130); and one C-130.

To the U.S. security analysts, government officials, and airline business professionals I’ve interviewed, these missing airplanes are a security threat. “Any aircraft that is not accounted for represents a concern because of the unique capability of aircraft to bound over the top of terrestrial defenses, go beyond ports, and be able to penetrate directly into large continental spaces,” says a former government employee who requested anonymity. “Timothy McVeigh [the Oklahoma City bomber] showed us what can be done with a Ryder truck. And that was just a truck. I know what [terrorists] can do if they put their minds to it.”

Because missing airplanes exist in a world of criminal investigations and classified information, almost no one who is knowledgeable about them will discuss the problem on the record. Many say that they “don’t want the bad guys to know what we know.” Some want to protect their security clearances or their jobs within the intelligence services and commercial aviation; others are fearful of retaliation by criminals they know to be involved with the aircraft. Kip Hawley, director of the U.S. Transportation Security Administration from 2005 to 2009, was one of the few who agreed to be quoted.

“We’re pretty well protected against somebody with a stolen airframe that is flying around, entering our airspace, that is not identified properly and headed to crash into a building,” says Hawley. “There is a well developed and not all secret [plan]. If there are planes in U.S. airspace, it’s very simple to shoot [them] down. It’s not something that’s done lightly, [but] the system is greased, it’s rehearsed. And they literally have open phone lines 24 by 7.

“The one that I most worried about was if al-Qaeda were to get access to a nuclear weapon,” he says. “[They] wouldn’t dump it into a shipping container and let it float across one of the oceans for three weeks. They would put it into an airplane and call it a freighter or call it something else and then fly it to its destination and of course never land. It was in those scenarios that we were most interested in missing aircraft.”

Are missing aircraft more likely to be involved in a terrorist attack than a legitimately recognized airliner or cargo aircraft? “It’s hard to say,” says a former member of the intelligence community. “The folks we’re talking about here are very patient. They could make use of an airliner that has been acquired by theft. But they could also hijack an airliner, or…. Take the case of Osama bin Laden, who was connected to a father who had so much money. Just buy an Airbus, buy a Boeing. Pick your model. Legitimately license it and go fly off in it and do something bad with it.

“The thing about missing aircraft is that they are an uncontrollable unknown. You can put security measures in place to counter a hijacker, and you can put security measures in place to do a background check on somebody buying a large aircraft, but the missing airplane is in the realm of ‘You don’t know what you don’t know.’ They’re a wild card.”

Ghost planes were sufficiently troubling to U.S. security services that in 2003, in the early stages of the N844AA investigation, President George W. Bush was given daily briefings on the case. N844AA had been converted from a passenger airliner to a freighter, and ten 500-gallon tanks had been installed in the cabin so the aircraft could haul diesel fuel to Angolan diamond mines. The realization that a flying gas tank had gone missing, just two years after the 9/11 attacks, electrified the intelligence community.

By 2007, the U.S. Air Force had in place a program called SUDDEN SPIRIT to analyze information about civilian aircraft. It was highly classified, as is the intelligence agency it spawned. According to Air Force spokesperson Major Mary Danner-Jones, “The people and mission formerly assigned to SUDDEN SPIRIT now function as the Civil Aviation Intelligence Analysis Center,” a program established in July 2011. I was not allowed to interview anyone within the CAIAC. When I asked what the employees do, Danner-Jones sent a statement: They “conduct…analysis that enables monitoring of foreign civil aviation assets involved in terrorism, weapons proliferation, and [Weapons of Mass Destruction] trafficking.” How many people work for the CAIAC? Classified. Are any of them looking for ghost aircraft? Classified. Are they trying to find out who operates them? “For obvious reasons, we don’t discuss the specifics of how we conduct intelligence.” There is no information to suggest that the CAIAC has field agents looking for ghosts. From the website of a software company that counts the CAIAC among its customers, Intelligent Software Solutions, I deduce that the agency analyzes data. ISS “provides the CAIAC with analytical tools and experienced all-source Intelligence Analysts to perform in-depth research and production of timely strategic analysis.” A slogan from another software company that supported SUDDEN SPIRIT: “We connect the dots you didn’t know were there.”

A former intelligence officer who requested anonymity believes his previous colleagues aren’t paying enough attention to missing airplanes. “The government has all this freaking expensive stuff—satellites and gadgets and shadowy operations—that collect all this secretive information. Almost none of it is focused on civil aviation. They’re focused on the same crap they’ve been focused on forever, which is foreign military capabilities. If you want to know about some foreign fighter jet, there are probably thousands of people focused on that. If you want to know [about] an airliner, there might be one guy in the whole government.”

The people who know what’s happening in civilian aviation, he adds, “are people in the private sector in the aviation industry.”

That would be Alexandre Avrane, for one, creator of the online catalog AeroTransport Data Bank. When used-aircraft brokers, UN investigators, aid organizations, journalists, or intelligence agencies want information about aircraft capable of carrying 30 passengers or more (or the equivalent tonnage in freight), they often turn to Avrane’s database, which currently has more than 1,000 subscribers and holds records for 81,554 aircraft. Avrane, who lives in Paris, has been adding to the database since 1997. He and his staff rely heavily on computerized aircraft tracking technologies, aviation websites and publications, and a worldwide network of informants, but their greatest tool is probably Avrane’s passion.

The Internet has made it easy to track the current movements of aircraft. Now anybody can punch a flight or tail number into a smartphone—suitable apps can be downloaded from FlightAware.com, PlaneFinder.net,

and other airplane tracking sites—and follow an airplane from Hong Kong to L.A. to Moscow on a tiny map. Digital photographs of aircraft landing at airports around the world are posted on websites even before the transports can shut down their engines. Despite these tools, large civilian aircraft still vanish—and not because they have crashed.

On his database, Avrane tags them “UFOs”—ultimate fate obscure. “An airplane is either supposed to fly, or it’s stored,” he says. “For large aircraft, I put the UFO tag when a significant amount of time has elapsed when it hasn’t been flying, but there is no indication that it’s been stored.” He considers two years a significant period.

Still, he believes that that only a very small fraction of the aircraft he lists as UFOs are used for criminal activities. “Most of the UFOs are just quietly scrapped somewhere,” he says.

The somewhere, according to Avrane and several others I interviewed, is most frequently Africa. “There’s a lot of missing airplanes, and usually the answer is they went to Africa, wrecked somewhere, and were made into pots and pans,” says a former government employee who asked that his name not be used. “It’s about the hardest place in the world” to find an airplane.

“Ever see those guys chop up an airplane with an axe?” asks pilot Brad Randall. Randall spent years in the Democratic Republic of the Congo (DRC) flying airliners and corporate aircraft. “It takes them about a month. About six guys with an axe. It’s not like here where they have those claws that cut metal. Just with an axe, piece by piece. I watched them chop up a 707 in Lubumbashi [in the DRC]. Every time we’d arrive, piece by piece, the airplane would be apart until it was all gone. It was incredible.”

But not all are chopped up. In a 2008 report on weapons shipments in Africa, The Arms Flyers: Commercial Aviation, Human Rights and the Business of War and Arms, is a photograph, taken on December 5, 2005, of an Ilyushin Il-76 at Entebbe International Airport in Uganda. On the aircraft’s tail, the name of a company has been painted over and no registration number is visible. The caption reads, “It has not been possible to identify this aircraft, nor has the Civil Aviation Authority of Uganda been willing to provide information about it.”

The search for Malaysia Airlines flight MH370, which disappeared last March with 239 people on board, makes clear one of the reasons that something as big as an airliner can simply vanish: Most of the oceans are not covered by radar. The Boeing 777 dropped from sight after it executed a bizarre change in course as it entered Vietnamese airspace over the South China Sea. The last sightings were by Thai and Malaysia military radars. Investigators believe that the radar data, together with Inmarsat signaling messages, placed the aircraft in a southern area of the Indian Ocean at the time when its fuel would have been exhausted. Last June, the Australian Joint Agency Coordination Center resumed the search, targeting an area larger than 20,000 square miles.

It’s possible that once all airliners are equipped with ADS-B (Automatic Dependent Surveillance—Broadcast) transmitters, which broadcast locations with more precision than current transponders (see “Lost in America,” Oct./Nov. 2011), airliners will no longer go missing. And in the wake of MH370’s disappearance, some are calling for better satellite tracking that could follow airliners as they cross oceans. Alexandre Avrane doubts that technology will make a difference. “Even if ‘new’ satellite tracking systems cannot be disabled by cockpit crews, they will still require some maintenance and can be removed or disabled by maintenance or during overhaul,” he emailed. He doubts that airlines in poorer countries will spend the money to install the tracking technology.

I asked one of the security professionals who was involved in the search for N844AA, the 727 that disappeared after leaving Angola, if he thought that advances in technology could end the disappearance of airliners. “We said that after 844AA,” he emailed.

“ ‘Modern’ airplanes with Mode-S, SATCOM, etc., won’t disappear. Until one does.”

A former intelligence professional thinks it likely that MH370 will be found and that N844AA may already have been: “It’s likely because there are eyes and ears everywhere. Eventually, over time, someone would run across it. There are enough extraordinary national assets that it would be extremely difficult for something to hide. [It is possible that N844AA] has been identified and either determined not to be a threat or turned into a ghostly asset—that is, not acknowledged as having been found but used by friendly forces.” In Avrane’s database, the last owner listed for the two missing civilian C-130s is the CIA.

Few aircraft disappear as spectacularly as MH370. Most disappear in a much quieter way—by acquiring new identities.

Since 1947, the International Civil Aviation Organization has required operators to register aircraft with a country’s civil aviation authority and to carry certificates of registration and airworthiness, pilots’ licenses, and other paperwork. (The ICAO assigns registration prefixes to each country, which can be a letter or letters, or letters and numbers; the U.S. prefix is “N.” ) But enforcing compliance with ICAO requirements is up to each country, and standards vary. “There are plenty of areas worldwide where ATC [air traffic control] is almost non-existent, airport staff do not care, or can be bribed,” says Avrane.

A 2008 UN report on the flow of weapons into the Democratic Republic of the Congo assessed the DRC’s ability to track its aircraft and states that there were “20 aircraft with an obviously incorrect registration number and, most importantly, 89 aircraft whose manufacturing number is missing or incorrect.” The manufacturing, or serial, number is the key to an airplane’s identity. Although a large aircraft can easily have a half-dozen or more registration numbers over its lifetime, the serial number is included on an airplane’s data plate (along with the manufacturer’s name, the model of the aircraft, and its date of construction), which is installed by the manufacturer as the aircraft is being built. Once attached, typically near the cockpit, where it can be easily seen, the data plate is supposed to stay with the aircraft. If it’s missing or has been tampered with, that can be a sign that someone is trying to hide the aircraft’s real identity in order to avoid mandatory and expensive maintenance checks, or to disguise its involvement in crime or sanctions violations.

“Data plates are easy to forge,” says a pilot with a long history of flying in African conflict zones. (Because he has tampered with data plates himself, he asked that his name not be used.) “I once upped the [Zero Fuel Weight] on a C-54D model by making a plate and quoting some MIL spec number increasing the ZFW to the same as a G model. It is still in that C-54 to this day.”

In 2003, authorities found that a data plate on an aircraft in the DRC had been switched. On May 27 of that year, an AN-12, registered as 9L-LCR in Sierra Leone, was attempting to land in Goma, a city in the eastern region of the DRC. The Antonov landed long, sustaining damages too extensive to repair. After salvaging what was possible, airport workers dumped the remains of 9L-LCR in a nearby empty field.

A few weeks after the crash, a different AN-12 was registered in the DRC as 9Q-CGQ. UN investigators determined that 9Q-CGQ’s serial number, and therefore its identity, actually belonged to 9L-LCR, which was still in the Goma field. Somebody switched data plates, but the UN investigation could not determine why.

What if a ghost airplane were to show up in U.S. airspace? The Federal Aviation Administration is one line of defense against that. With its International Aviation Safety Assessment program, the FAA evaluates the civil aviation authorities of all countries with air carriers that fly into or have applied to fly to the United States. If the aviation authority does not meet ICAO safety standards, its airplanes are denied access.

Although Cuba has never petitioned to land in the United States, Cuban carrier Cubana overflies Florida and four other states on a scheduled route to Canada. In March 2011, a forum on an airplane tracking website chattered that a Cubana Tupolev Tu-204 on that route was sending a transponder code that identified it as North Korean airliner P-632. A search of AeroTransport Data Bank showed that two transports, Air Koryo’s P-632 and Cubana’s CU-C1703, both Tu-204s, were using the same transponder code.

Because the code is programmed at the factory when the transponder is installed, Alexandre Avrane dismisses the duplication as a Tupolev screw-up. But while amateur Internet trackers noticed the odd code, would any of the U.S. air traffic control centers along Cubana’s route have caught it? They had another chance last August. After more than a year of inactivity, CU-C1703 began flying its route again. According to the FAA, Cubana airliners routinely communicate with FAA air traffic control facilities as they fly from Cuba to Canada. On the code transmitted by CU-C1703, spokesperson Kathleen Bergen emailed the FAA’s position:

“The Hex code is part of the aircraft’s Certificate of Registration, and generally remains with the aircraft, and is not changed. A Hex code is associated with the aircraft, not with the company or the country operating the flight. The Russian-built aircraft could have a North Korean Hex code because it was flown by North Korea before being sold or transferred to Cuba. Also, the original Russian transponder could have been replaced with North Korean equipment.”

The statement does not address the second aircraft transmitting the same code. What is obvious is that one aircraft, by sending a false identifier, can pretend to be another.

The most recent U.S. aircraft to disappear, according to Alexandre Avrane’s database, is LY-AWH, a Boeing 737 that dropped out of sight in February 2013. The “LY” designates an aircraft registered in Lithuania. Somewhere, somebody knows where to find LY-AWH. But more important than that person’s identity or the airplane’s current location is this: When LY-AWH reappears, what will it be doing?