"The first thing we did was laughed because who would believe such a story," Hanson said. "But then we quickly decided we better go down and check it out."
Weeks later, Hanson and fellow archaeologist Mark Hungerford surveyed the cemetery site and found numerous holes, evidence of unauthorized digging.
While records show the cemetery had been disinterred twice by the Army in the late 1800s, it wasn't known how many bodies remained. Hanson said ground-penetrating radar revealed the Army left behind about one-third of the bodies.
A lack of funding and various federal procedures delayed the excavation until last summer.
Brecheisen's son told authorities where the mummified remains from his father's home were, and a person who hasn't been publicly identified handed them over, including a more-than-century-old skull packaged in a brown paper bag. Alberts said that skull, which still had hair attached, was the one he'd seen years earlier.
Authorities also found some Civil War and American Indian artifacts in Brecheisen's home, but the display rooms that showcased Brecheisen's collections had already been emptied out and auctioned off by his family after his death, Hanson said.
Investigators believe Brecheisen did most of his looting alone, but they also know he dug with close friends and family at the Fort Craig site. Some who accompanied him led authorities to the grave sites, Hanson said.
Brecheisen was a decorated Vietnam veteran and flew for the Air National Guard during a 26-year military career. His family described him as "one of the state's foremost preservationists of historical facts and sites" in his obituary.
Those close to Brecheisen said his looting may have been motivated by anger toward the Bureau of Land Management, but no further details were available. Alberts described him as a collector; it wasn't clear whether Brecheisen sold any of the items.
Investigators believe he also dug up grave sites in Fort Thorn and Fort Conrad in southern New Mexico as well as prehistoric American Indian burial sites in the Four Corners region.
Hungerford said they also believe he may have taken the Fort Craig burial plot map, which is missing from the National Archives.
The criminal case against Brecheisen was closed upon his death and there are no plans to investigate his family members, assistant US Attorney Mary McCulloch said.
Alberts said he asked Brecheisen to come clean.
"I had urged him to simply return the remains, about 10, 15 years before he got ill. I offered to act as an honest broker to the deal and see that they were returned, but I didn't get a response," Alberts said. "I didn't want to get a friend in trouble."
He added: "But you look back and think you would have done everything differently if you would have known everything was going to disappear."