The Advanced Aviation Threat Identification Program, as it's called, "collected video and audio recordings of reported U.F.O. incidents".
That footage includes one of an undated encounter with "an aircraft surrounded by some kind of glowing aura travelling at high speed and rotating as it moves," The Times wrote.
AATIP reportedly started in 2007 to study potential unknown military threats, and was funded by nearly US$22 million of Department of Defence "black money".
DoD officials told The Times and Politico that it shut down the program in 2012. But Luis Elizondo, a military intelligence official who ran the research effort, allegedly continued its efforts afterward.
Elizondo resigned in October, reportedly in protest of secrecy surrounding the program. He now helps run Stars Academy of Arts and Science, a startup company that researches UFOs.
"These aircraft … are displaying characteristics that are not currently within the US inventory, nor in any foreign inventory that we're aware of," Elizondo told CNN on Monday.
"My personal belief is that there's very compelling evidence that we may not be alone. Whatever that means."
"If you see something in the air that you don't understand, and you're the guy in charge of the Air Force, you want to know what that is. It doesn't have much to do with aliens, necessarily," Shostak told Business Insider of AATIP's purpose.
"But despite more than a half-century of this, the really good evidence that we're being visited still has failed to surface."
Travelling hundreds of light-years 'to do nothing'?
But that isn't the only reason Shostak is sceptical of alien visitation claims.
If the probe was aimed at Proxima Centauri – the closest star to Earth besides the sun – it'd take nearly 75,000 years to reach that system, since it's roughly 4.24 light-years away from us.
Shostak said that alien civilisations would know about our existence if they're within about 35 light-years of Earth, since we haven't been sending signals into space for very long.
"The only way they could know that is to pick up, for example, signals from our transmitters – television, radio, radar, all that stuff. But those signals have been going out only since the second World War," Shostak said.
"So if they're more than 35 light-years away, there hasn't been enough time for our signals to get to them, and for them to decide, 'Well this is worth the money to go down there and fly around.' Because they can't go faster than the speed of light, and they probably can't go the speed of light."
Within a generous 50 light-years, there are only about 1,400 star systems.
"That sounds like a big number, but it's a very small number if you're looking for intelligent beings," Shostak said. "Unless they're the next star system over, which is statistically rather unlikely."
Assuming that aliens regularly visit Earth defies logic in other ways, too. In nearly all credible reports of UFO sightings, there's no interaction with the witness (aside from claims of alien abductions, which evidence suggests are hallucinations caused by episodes of sleep paralysis and possibly abuse).
"They're the best house guests ever. Because if they're here, they're not doing anything … They send a huge fleet of spacecraft, preferably shaped like dinner plates, just to fly around and get people agitated but otherwise not to do a thing," Shostak said. "It is a little odd that aliens would come hundreds and hundreds of light-years to do nothing."
Shostak compared this to Europeans discovering America, but never troubling any Native Americans: "They don't try and take any of their land, they don't bring any disease, they don't do anything; they just sort of walk around at the fringes of their settlements, leading to puzzling sightings, but that's it."
On top of this, Shostak thinks the reasons to visit Earth aren't very convincing.
"I always ask, 'Why are they here now?' They weren't visiting the founding fathers in the late 1700s, they're visiting us," he said. "The Romans weren't troubled by the aliens visiting. It doesn't make very much sense why they're here now."
Rooting out the nature of UFOs
Shostak rejects the notion that the news about AATIP and the Pentagon's footage constitute definitive proof of aliens.
About 90 percent of UFO sightings have explanations, he said, and that still doesn't mean the other 10 percent are aliens.
"It just means they're unexplained," he said.
"It isn't that one shouldn't look into these – of course, if there really is something here, it'd be extraordinarily interesting to find out. But the fact that there are cases that are hard to explain and that sound rather convincing would be true no matter what the premise."
Sara Seager, a planetary scientist at MIT who hunts for signs of habitable planets, echoed this idea in The Times' story, telling the newspaper "what people sometimes don't get about science is that we often have phenomena that remain unexplained."
Another area of scepticism for Shostak is that AATIP contracted out much of its work to Bigelow Aerospace in Nevada. The real-estate billionaire Robert Bigelow runs that startup and is friend of former Nevada senator Harry Reid, who started AATIP – in part, according to the Times, due to persuasion from Bigelow.
Shostak said he's met Bigelow, and describes him as a "very likable guy" who is a passionate believer in alien visitations, but "not a scientist".
"If you were investigating some phenomenon that you're not sure whether it's for real or not, but it would be extraordinarily important if were real … you would want somebody sort of impartial, I would think," Shostak said.
"Giving this case to somebody who already knows what the answer is is maybe not terribly objective."
And then there are the UFO sightings themselves, which likely have far simpler explanations than alien visitations. For example, they tend to spike in the summer for a variety of reasons.
Issues with camera hardware, unfamiliar optical effects, atmospheric phenomena, bright stars and planets, and the presence of unmanned aerial vehicles are all common explanations.
Though AATIP's unmasking has vindicated many claims by the UFO community that the government is covering up its research, it "may be a situation where they should have been careful what they wished for," Shostak said.
"The government said, 'Well, yeah – we did have a program, and we did cover it up, but we didn't find anything.'"
Indeed, an anonymous senior intelligence official told Politico that AATIP began mostly to root out the existence of unknown Chinese and Russian military technologies.
But after a couple of years, "the consensus was we really couldn't find anything of substance," the official said. "They produced reams of paperwork. After all of that there was really nothing there that we could find."
This article was originally published by Business Insider.