The investigation made soldiers into scapegoats and even the service admits it was badly managed from the start.
The May 22 episode of the news program examined the Army's extensive review of the Guard's Recruiting Assistance Program, an effort launched in 2005 to help the service meet manpower needs during the Iraq war.
The program paid soldiers who signed up as informal "recruiting assistants" between $2,000 and $7,500 for each person they helped to enlist. The service suspended the effort in 2012 after auditors flagged suspect payments.
That same year, the Army set up a special unit of 60 full-time agents to investigate every one of the 105,000 soldiers who received bonuses.
So far, the Army has spent nearly $28 million to uncover $10 million of alleged fraud, "60 Minutes" reported. Over 100,000 soldiers have been cleared of wrongdoing with more than 4,000 still under investigation.
"When you zero in on the time that this program was initiated in 2005, the Army was under a lot of stress. We were fighting in two wars. The National Guard was 20,000 soldiers under strength and attempting to grow," Lt. Gen. Gary Cheek, director of the Army Staff, told David Martin of CBS News.
"We had a program with the best of intentions, but unfortunately it was poorly designed," Cheek said. "We left ourselves vulnerable to fraud."
The National Guard Association of the United States released a statement about the episode, criticizing the conduct of the investigation that treated many soldiers as guilty until they could prove their innocence.
"Scrutiny of this lengthy investigation is long overdue. What the Army calls the largest investigation of fraud in the history of its Criminal Investigation Division (CID) has been largely fruitless and shameful," retired Maj. Gen. Gus Hargett, the NGAUS president, said in the statement.
Lt. Gen. Flora Darpino, the Army's top lawyer, defended the investigation that went after soldiers who took advantage of the program to commit criminal misconduct.
"When it comes to crime, it isn't really about the cost of what it takes to investigate," Darpino told the news program. "It's making sure that people are held accountable for criminal misconduct. And that's why we investigate."
The investigation has indeed uncovered wrongdoing.
In one case in Texas, former Spc. Xavier Aves, of San Antonio, collected $244,000 alone, according to the program. He pleaded guilty to abusing the program by referring people who had already enlisted and providing kickbacks to recruiters who supplied him with their names and Social Security numbers, it reported. He was sentenced to serve almost five years in prison., it reported.
But many other soldiers have been brought up on charges that failed to hold up in court.
Master Sergeant Jerry Wilson is one of the 105,000 soldiers who fell under investigation, according to the program. He collected $43,000 from the program for recruiting 22 soldiers, it reported. Wilson, who faced up to 12 years in prison, defended his innocence and his decision to go to trial, it reported.
"Why would I go to court and put myself through everything I put myself through if I didn't think I was innocent?" he told "60 Minutes."
Wilson's trial lasted four days, and he was found not guilty of theft, but his troubles didn't end after the trial, according to the program.
The commanding general of the Colorado Guard "placed a reprimand in Wilson's file, killing his chances for promotion, according to "60 Minutes." It cited "compelling and substantive evidence that you defrauded the government," the program reported.
Wilson responded by accepting "some responsibility" saying "if I could go back and do it all again I would keep a very specific record of everyone I talked to," according to the segment. But he disputed he had acted "through nefarious means," it reported.
Many Guard members, "thinking they did nothing wrong, have cooperated with investigators, only to face criminal charges for minor violations of program rules that changed multiple times," Hargett said in his statement.
"Those in our ranks who intentionally defrauded the taxpayers deserve to be punished, but this investigation appears no longer to be about fraud. It has become an increasingly futile attempt to make ridiculous allegations seem a little less ridiculous, no matter what the cost," Hargett said "This investigation has needlessly harmed soldiers and their families. It needs to end."
--Matthew Cox can be reached at email@example.com.