IOWA CITY, Iowa (AP) – A 1990 theft of historically significant Native American remains by a national monument superintendent entrusted with protecting them was larger and more harmful than previously acknowledged, internal National Park Service documents show.

After decades of investigations and cover-ups, the case is scheduled to end in a federal courtroom Friday when retired Effigy Mounds National Monument superintendent Thomas Munson is sentenced for carrying out the theft. The 76-year-old has apologized and hopes to avoid a prison sentence.

But documents obtained by The Associated Press under the Freedom of Information Act point to wider problems at the federal park along the Mississippi River in northeast Iowa. A series of superintendents were warned that the museum’s entire collection of human bones had gone missing under Munson, but they did little to find them and failed to notify affected tribes. Even the current superintendent called it a devastating “debacle” that would hurt the agency for years.

“The one conclusion that can’t be argued by anyone is our lack of competence as an agency,” one National Park Service manager told an investigator in 2012, calling the case the “most glaring example” of that incompetence.

The documents shed light on Munson’s motive for stealing the bones, which were from more than 40 Native Americans who lived and died in the area between 700 and 2,500 years ago. The bones had been dug up from sacred tribal burial sites during archaeological excavations from the 1950s through the 1970s and were kept in the museum’s collection.

In 1990, Munson was worried about the impact of a new law that would require museums to return the remains of ancestors to their affiliated tribes along with any sacred objects with which they were buried.

Munson wanted all human remains removed before the law went into effect so the monument could keep its collection of burial objects, which he saw as more valuable than the skeletal fragments, documents show. In July 1990, he ordered subordinate Sharon Greener to pack them up in two boxes and help load them in his car. He drove them to his home across the river in Prairie du Chien, Wisconsin, where they sat in his garage for the next two decades and suffered damage due to “wildly inappropriate storage conditions,” records show.

Munson denied stealing the bones for years, but returned one box in 2011 after the agency launched another investigation. A federal agent found the second box during a search of Munson’s garage the next year. He pleaded guilty earlier this year to embezzling government property. He has agreed to spend one year on home detention and 10 weekends behind bars in a plea agreement, but his attorney says his declining health will make any period of incarceration difficult to serve. He will also pay $108,000 in restitution to the park service for costs of the investigation and repair of the bones.

The documents show that, shortly after Munson retired in 1994, his successors learned about the disappearance of the remains. Yet they failed to find out what had happened. “What a mess, huh?” one official wrote in a 1996 email.

The agency hired an outside contractor in 1998 to investigate but the findings were inconclusive, showing only that the remains were unaccountably missing.

Munson gave several shifting explanations for what might have happened to them over the years: that they were taken to the agency’s Midwest Archaeological Center or may have been inadvertently thrown away. He once claimed to receive a directive from superiors to get rid of them.

Yet the 12 tribes affiliated with the monument were not told that they had gone missing until Munson returned the first box in 2011. They were outraged.

“We need a head on a plate,” one tribal representative told monument officials, accusing them of a cover-up.

The agency responded by firing Greener, who appealed and argued she was being made the scapegoat after trying for years to bring the theft to light. Her attorney said that she “told everyone in authority about that removal” but “no one cared enough to take meaningful action,” documents show. The agency later quietly rescinded her termination and allowed her to retire.

Current superintendent Jim Nepstad, who finally helped uncover Munson’s theft, wrote in a memo that the case “has, and will continue to cause, profound damage to the credibility and reputation of the National Park Service.”

“There will eventually come a day when this story likely sees the light of day, and at that time the National Park Service will be confronted with the difficult task of defending itself against the shameful actions of some of its employees,” he wrote. “I and my successors – and the agency itself – will be dealing with fallout from this debacle for years to come. The offense of improperly removing the remains of more than 40 people is serious enough, but the consequences of covering up the offense and protecting the primary offender has made a very bad situation far worse.”