From 2007 to 2012, a small team of military investigators looked into sightings of unidentified flying objects—yes, UFOs—from an office deep inside the Pentagon....

From 2007 to 2012, a small team of military investigators looked into sightings of unidentified flying objects—yes, UFOs—from an office deep inside the Pentagon. The Advanced Aerospace Threat Identification Program, championed by former U.S. senator Harry Reid, paid contractors to analyze close encounters between military pilots and mysterious airborne objects.

Some of those close encounters probably involved secret military prototype front-line pilots didn’t know exist. Others, however, remain unexplained — and could be revolutionary for human civilization.

“Just because something’s unexplained doesn’t mean that it’s extraterrestrial, of course, but I never say never,” Nick Pope, who ran the British military’s own UFO investigative unit in the early 1990s, told me via email. “Extraterrestrial visitation might be unlikely, but if a single case turned out to be true, it would be a game-changer.”

One 2004 incident, in particular, has befuddled skeptics. Two U.S. Navy fighter pilots flying off the coast of southern California tracked an airliner-size, cigar-shaped object that appeared to hover and maneuver in ways that seem to exceed conventional aeronautics. “I have no idea what I saw,” David Fravor, one of the pilots, told The New York Times.

“There are still those observations that defy explanation—observations by highly trained individuals such as fighter or airline pilots who would recognize aircraft shapes and aircraft movements,” Luis Elizondo, the head of the Advanced Aerospace Threat Identification Program and related UFO efforts until his October resignation, told me via email.

“The basic instinct of intelligence personnel looking at the most convincing UFO sightings is to assume that they’re secret prototype aircraft or drones, developed either by another nation, or by another part of the government—but in a situation where the information is so compartmentalized nobody else can get access,” Pope said.

“Another theory is that some of these sightings are attributable to some sort of atmospheric plasma phenomenon that science doesn’t yet fully understand,” Pope added, using the scientific term for electrified air.

“Many UFO sightings in the southwest United States during the 1980s were actually secret advanced military aircraft such as the Lockheed F-117 and Northrop Grumman B-2,” Elizondo said.

There has been no shortage of rumored or confirmed, high-performance military prototypes in recent years that could account for UFO sightings. The U.S. Air Force secretly developed the RQ-170 stealth spy drone in the early 2000s, finally admitting to its existence only after a photographer spotted one at an airfield in Afghanistan in 2007. It’s unclear whether sightings of the RQ-170 explain any recent UFO reports.

More recently, the Air Force has been working on a bigger and ever stealthier spy drone called the RQ-180, along with the new radar-evading B-21 bomber. In 2014, a mysterious, wedge-shaped aircraft—possibly an early technology demonstrator for the B-21 program—was photographed flying over Kansas.

The military and the defense industry have also been hard at work on so-called “hypersonic” aircraft and space-planes capable of flying at speed exceeding Mach 5. Some of those efforts are public. Others, such as Lockheed Martin’s self-funded SR-72 hypersonic spy plane, remain cloaked in secrecy.

The abundance of secret prototypes plying American skies gives plenty of cover to government investigators and skeptical outsiders whose impulse is to dismiss possible evidence of alien life. “That said, there are those in government—including, clearly, some of the intelligence officials who worked in the AATIP—who are prepared to think the unthinkable, and say that some of these things might be extraterrestrial,” Pope said.

The 2004 video seems unexplainable now. But remember, many similarly mysterious UFO sightings in the past turned out to be military prototypes. Maybe aliens really are buzzing Planet Earth. But if history is any guide, it’s more likely the Pentagon’s own advanced aircraft that are making surprise appearances in front of baffled pilots.