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When FBI Agent Tim Carpenter first entered the basement of missionary Don Miller's rural Indiana farmhouse during a 2014 raid, he says it was "a jaw-dropping moment."

Miller, an amateur archeologist, had amassed tens of thousands of ancient artifacts from around the world — as well as thousands of human bones, most believed to be Native American in origin.

"A scene kind of unfolded in front of me, and I start seeing just row after row after row of artifacts and, you know, floor-to-ceiling shelves," Carpenter, head of the FBI's art crime team, told As It Happens guest host Susan Bonner.

"Clearly, we were not prepared for the amount of human remains that we discovered on the property."

Throughout the FBI's nearly five-year investigation, Carpenter and his team have partnered with archeologists, anthropologists and Native American tribal officials in the hopes of returning the artifacts — and the remains — to their countries and tribes of origin.

Now they're going public with the findings in the hopes of speeding up the process.

"The goal of this investigation for us has always been the repatriation of these artifacts and the human remains that we recovered," Carpenter said.

"Unfortunately, we've not reached as large an audience with our partners on this as that we'd hoped."

Who was Don Miller?

Miller, 91, was a world-travelling Christian missionary, military vet and amateur archeologist who was known in the community for his museum-like collection of international treasures.

He kept most of his artifacts on display in glass cases at his Waldron, Ind., farmhouse and would often invite local reporters, Boy Scouts and other residents to come for tours, reports CBS News.

He was also something of a local legend, having claimed he was involved in the Manhattan Project that developed the world's first atomic bomb, according to the Indianapolis Star. He died in 2015.

The FBI seized 7,000 items from Miller's home. (FBI )

A year earlier, the FBI got a tip that many of his worldly possessions were, in fact, ill-gotten.

In a six-day raid of his home, federal agents found 42,000 artifacts from North America, South America, Asia, the Caribbean, Papua New Guinea and China, and seized 7,000 of them.

Miller smuggled some of those items into the country in violation of state and federal law and international treaties, according to an FBI news release.

Other times, he allegedly resorted to "outright looting."

"He told me that he got his passion or his interest in archeology or collecting artifacts from walking the desert around Los Alamos in New Mexico and finding arrowheads and pieces of pottery," Carpenter said.

"That's kind of what got him hooked on it. And, you know, I think from there it just kind of grew."

Indigenous remains 'treated as curiosities'

The collection also contained 500 sets of "predominantly Native American" human remains that appear to have been looted from Indigenous burial grounds, Carpenter said.

It's not clear whether Miller dug them up himself or bought them on the black market.

Indiana University-Purdue University Indianapolis graduate students help take care of the recovered artifacts. (FBI)

The theft and display of Indigenous remains has long been a concern for Indigenous people in the Americas and around the world.

"All too often here, we have been treated as curiosities rather than a people," Pete Coffey, a tribal official with North Dakota's Mandan, Hidatsa and Arikara nations who is working with the FBI, told CBS News.

"They could very well be my own great-, great-, great-, great-grandfather or grandmother.... I characterize it as being ripped out of the Earth."

In 1990, the U.S. passed the Native American Graves Protection and Repatriation Act, making it a crime to buy or sell Native American remains.

In Canada, First Nations and developers repeatedly butt heads when pre-settler burial sites are discovered on private or commercial property.

Now the FBI finds itself far outside its wheelhouse, working on archeological identification, preservation and repatriation.

They've rented a space in Indianapolis to house the items, and hired a team of anthropology and museum studies graduate students to take care of them.

'It was his wish that we returned these objects'

Authorities have set up an invitation-only website for tribes, experts and international representatives to scour through the catalogued findings.

The bones are not displayed on the site, Carpenter said, but anyone with a legitimate claim is encouraged to contact the FBI.

Some items have already been returned to governments and museums in Canada, Colombia, Ecuador, New Zealand and Spain. On Wednesday, 361 artifacts are being repatriated to China.

The FBI says 361 artifacts, including this one, were repatriated to China. (FBI)

But others — especially the bones — are harder to identify.

"We typically won't do DNA analysis on the bones, and that's out of respect and at the request of Native tribes that we've consulted with," Carpenter said.

"Taking DNA analysis requires some invasive procedures that is further offence to the ancestral remains, and so we're not willing to do that. So we rely largely on osteological analysis, and that can only give us a piece of the picture."

As for Miller, Carpenter said he expressed regrets about his exploits during his final years.

"It was his wish that we return these objects back to the rightful owners," Carpenter said. "So I think we can discern from that that, you know, he was trying to do the right thing at the end."

Written by Sheena Goodyear. Interview with Tim Carpenter produced by Ashley Mak.