“I mean this man, he’s an amazing piece of history,” Amy Mohr, a friend of Miller’s from church, told the Indianapolis Star in 2014. “He’s an artifact himself.”

But when the FBI’s art crime detectives showed up and began sifting through Miller’s extensive collection in April 2014, suspecting that many of the relics carefully laid out in the cabinets had been obtained in violation of antiquities laws, they came across something that horrified them: about 2,000 human bones, nearly all of which are thought to have been taken from ancient Native American burial sites.

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“To the best of our knowledge right now, those 2,000 bones represent about 500 human beings,” Tim Carpenter, who heads the FBI’s art theft unit, told CBS News in an interview that aired Tuesday. “It’s very staggering."

Miller, a Christian missionary and ham radio operator who claimed to have worked on the Manhattan Project, died at age 91 in 2015, nearly a year after the FBI raided his home and seized about 42,000 items whose cultural value was said to be immeasurable. Until this week, officials had provided little information about the case, and had declined to go into detail about exactly what the art crimes detectives had found inside the prolific collector’s home.

Talking to “CBS This Morning” on Tuesday, Carpenter said that, before his death, Miller admitted that he had come by many of the items illegally, and that he had gone on unsanctioned archaeological digs all over the country and the world. He also came to agree that the artifacts should be returned to their proper homes. But because he died while the investigation was still ongoing, many aspects of his life — and the trove he left behind — are a mystery.

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For instance, CBS’s Anna Werner asked, why would anyone have so many human bones?

“I don’t know,” Carpenter replied, shaking his head. “I truly don’t know.”

The ghoulish crime of digging up long-dormant graves has been an ongoing source of frustration for Native American communities. Toward the end of the 19th century, both amateur and professional archaeologists began running roughshod over tribal burial grounds, excavating the skeletons of indigenous people who had died hundreds of years before. Some bone fragments were put on display in museums, while others were closely analyzed by anthropologists looking to test since-debunked theories of race science, such as the belief that intelligence was directly correlated with the size of one’s skull. It took nearly 100 years before the Native American Graves Protection and Repatriation Act was signed into law in 1990, making it illegal to buy or sell Native American remains.

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“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 Nation, told CBS. “They could very well be my own great, great, great, great grandfather, or grandmother. . . . I characterize it as being ripped out of the earth.”

Coffey is one of the tribal leaders working with the FBI to return the misappropriated remains to their original resting places, CBS reported. Experts say they think that most of the bones found in Miller’s home were removed from burial sites in North Dakota, and that many belonged to the Arikara tribe. It’s unclear whether Miller had shown off the remains to people who visited his home, and whether he had dug them up himself or purchased them from someone else who did.

Until Tuesday, the FBI had remained circumspect about the 2014 raid, which did not result in Miller’s arrest or any charges. At the time, officials said that they had received tips about his cache of treasures and were investigating to see whether any of the items were illegal for private citizens to possess. In addition to copious Native American artifacts, Miller had reportedly collected priceless relics from countries including Australia, China, Haiti, Peru and Russia, and stored them in outbuildings scattered around his remote Waldron compound as well as in his commodious basement.

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Robert A. Jones, the FBI special agent in charge of the case, told reporters at the time that Miller’s methods for procuring some of those objects had violated multiple laws and treaties, but also undercut that claim by acknowledging that the relevant statutes may not have been in place yet. After all, Miller had started his collection eight decades before, when he first found arrowheads on his family’s farm as a child.

Advocates for criminal justice reform and libertarian groups such as the Cato Institute were quick to criticize what they considered an overly aggressive approach from the FBI, arguing that the government had offered no evidence that Miller had done anything illegal. “The FBI plan is apparently to seize the contents of an elderly man’s lifelong hobby, then force him to prove he obtained each item in his collection legally,” Radley Balko wrote in The Washington Post.

Nearly five years later, the investigation is still ongoing, and experts anticipate that it could take decades to sort through the thousands of objects that the FBI seized, since determining their legality means first figuring out where and when each was purchased. Some of the artifacts have already been repatriated — Bogota’s City Paper reported in October that 40 pieces of pre-Columbian pottery, some dating to 1,500 B.C., had been ceremonially returned by the State Department after the FBI determined that Miller had smuggled them out of the country. Other artifacts have been sent back to countries such as Canada, Ecuador, New Zealand and Spain, the FBI’s Indianapolis bureau said in a tweet Tuesday. An additional 361 items from Miller’s collection will be returned to China this week.

Before splashy headlines in the national media labeled him a real-life Indiana Jones, Miller was known to Waldron and surrounding Rush County, Ind., as a larger-than-life figure who had a penchant for telling unverifiable stories and playing a 1927 Wurlitzer organ to entertain his guests. Speaking to the Star in 1998, he said that he had been stationed in New Mexico during World War II and assigned to the top-secret Manhattan Project, where he claimed to have witnessed the detonation of the first atomic bomb. When the war ended, he went on to spend 30 years working as an electrical engineer for the Naval Avionics Center in Indianapolis, while simultaneously making trips to build churches in Haiti and Colombia. After retiring at age 60, he and his wife, Sue, a former high school teacher, regularly traveled to impoverished countries to do missionary work.

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All the while, he filled up their home with historical curios, including a World War II-era Nazi helmet and a shrunken head whose provenance he did not fully explain.

A former co-worker told the Star in 2014 that Miller had used his ample vacation time at Naval Avionics to conduct amateur archaeological expeditions in far-flung parts of the world, and that he often came back with wild tales about his misadventures, including winding up in a Mexican jail and being interrogated by Libyan soldiers who thought he had been sent by the CIA. While those stories proved impossible to confirm, Mohr, his friend from church, recalled that Miller had tried to leave Haiti with a few cannonballs, and ended up getting stopped at the airport at the end of their mission trip.

In the months before his death, Miller had retreated from public life, residents told the Star. When a news crew from CBS showed up at the sprawling two-story house before Tuesday’s broadcast, his wife said that she was unable to comment on the FBI’s discoveries. A Chinese terra-cotta warrior statue was still standing outside the door.