 -- Mary Lacy was one of a team of four who walked through the home of JonBenet Ramsey just days after the 6-year-old beauty contestant was discovered dead in the house's basement in Boulder, Colorado, on Dec. 26, 1996.

Just around the corner from JonBenet's room on the second floor, an indentation in the carpet was spotted and chills ran down her spine, she told ABC News. "It was a butt print. We all saw it. The entire area was undisturbed except for that place in the rug," Lacy, who was then the chief deputy district attorney heading up the Sexual Assault Unit under Boulder County DA Alex Hunter, said. "Whoever did this sat outside of her room and waited until everyone was asleep to kill her."

The apparent presence of that indentation went on to help form a theory that Lacy believes to this day.

The morning after Christmas in 1996, JonBenet was reported missing by her parents after they said a ransom note was found in their home. Her body bound and her mouth covered with duct tape, JonBenet was later discovered in the basement. An autopsy concluded that the cause of death was asphyxiation due to strangulation. The coroner's report stated that a blunt object had hit her so hard, there was an 8-inch fracture to her tiny skull. The report also showed some damage to JonBenet's hymen, indicating possible sexual assault.

John and Patsy Ramsey, as well as JonBenet's brother, Burke Ramsey, were the only other people known to be in the house at the time of the slaying, and for years after her death, they were each trailed by a cloud of suspicion. John and Patsy Ramsey were at one point considered persons of interest in the case by authorities.

But in 2008, Lacy -- who by then had been named Boulder County DA and taken over the investigation -- surprised even some of the most seasoned of her fellow prosecutors by exonerating the family.

Now, for the first time in eight years, the former prosecutor is speaking out to ABC News about her decision to clear the Ramsey family as her exoneration letter has now come under scrutiny following a joint investigation by the Boulder Daily Camera and Denver's KUSA-TV/9News.

'Trying to Prevent a Horrible Travesty of Justice'

Former Adams County DA Bob Grant, one of a number of consultants on the case brought in early on by the Boulder County DA at the time, Hunter, told ABC News he was confounded by Lacy's 2008 decision. "This is craziness," he said. "This is not what prosecutors do. If prosecutors are going to exonerate someone they do it by charging someone else."

But Lacy didn't charge anyone else in the murder. Instead, armed with newly discovered DNA evidence found on JonBenet's long johns that Lacy said she believes belongs to JonBenet's unknown murderer, she sent the Ramseys a letter of apology. It read, in part, "to the extent that we may have contributed in any way to the public perception that you might have been involved in this crime, I am deeply sorry." The letter made international news.

The DNA evidence was discovered after Lacy sent the long johns to Bode Cellmark Forensics to be tested for touch DNA. She had attended a seminar in the summer of 2007 that explained the relatively new process. She felt it could advance the seemingly stalled case, she said.

Some Boulder Police Department detectives who had long worked on the investigation and still considered the Ramseys persons of interests were furious.

"Here’s what I was doing with the exoneration letter," Lacy explained. "I was trying to prevent a horrible travesty of justice. I was scared to death that despite the fact that there was no evidence, no psychopathy and no motive, the case was a train going down the track and the Ramseys were tied to that track."

In the 2008 letter, Lacy hung her hat on newly discovered touch DNA found on JonBenet's long johns, which she said was found to belong to an unknown male. Lacy argued that this unknown male DNA matched DNA found in two spots of blood in the crotch of JonBenet's panties. The unknown male DNA, reasoned Lacy, was the smoking gun that pointed to JonBenet's killer and that killer was not anyone in her family. Family members and 200 other potential suspects were excluded from the unknown male DNA found on the panties and long johns, she said.

Lacy's theory? When the Ramseys left to have Christmas night dinner with friends, they left the front door unlocked, and a male intruder simply walked inside and waited for hours for the family to come home. During that time, Lacy believes, he wrote the rambling two-and-a-half page ransom note.

That note referenced several lines from movies. "The Boulder police should have checked all of the video stores to see who was renting those movies and they never did," said Lacy.

However, the Boulder Daily Camera's investigation published Thursday found the DNA results in the Bode report are not necessarily as clear cut as Lacy concluded they were. According to the Daily Camera, they showed the Bode report to independent experts who say that the DNA samples from both the underwear and long johns may be composite samples from multiple people: JonBenet, an unknown male and, in one sample, a third unidentified person. To the extent composites were used in the search to identify the killer, the investigation states that the DNA profile "may be worthless as evidence." According to the paper, the possible presence of a third individual's DNA on the long johns has never been publicly revealed.

The experts also stated that the presence of the DNA on JonBenet's undergarments could have an innocent explanation because the "profiles were developed from minute samples that could have been the result of inconsequential contact with other people or transferred from another piece of clothing."

According to the paper, these opinions "cut both ways" on the competing theories of the case. They neither disprove the intruder theory nor "implicate or exonerate anyone in the family."

When asked about the impending Daily Camera report ahead of its publication Thursday, Lacy said she has taken criticism for her decision to write the exoneration letter in the past. "I've withstood worse than this," she said. "And it's nothing compared to what the Ramsey family has gone through targeted as suspects in their own daughter's murder." Lacy has not responded to ABC News' request for comment since the Daily Camera report was published.

Is JonBenet's Murder a DNA Case or Not?

There have been conflicting views over whether the mystery of JonBenet's murder can be solved by DNA alone.

Former Boulder Police Chief Mark Beckner, who headed up the department from 1998 to 2014, said in an "Ask Me Anything" session on Reddit last year that the investigation considered the DNA important, but that there was other crucial evidence in the case that couldn't be ignored.

"Mary Lacy, the DA who said the DNA exonerated them, made up her mind years before that a mother could not do that to a child, thus the family was innocent," Beckner wrote.

Stan Garnett, the current Boulder County DA, told ABC News that no case is ever solely reliant on DNA. "DNA is a part of the case," he said. "But you have to account for everything else. There were problems with crime scene, you have the ransom note ... you have debates about the cause of death -- to solve this case we have to account for all of that."

But forensic pathologist Lawrence Kobilinsky with the John Jay College of Criminal Justice, who has not worked on the case but who reviewed a summary of the Bode report put together by Boulder County investigator Andy Horita prior to the publication of the Daily Camera report, told ABC News that ignoring the unknown male DNA would be a huge mistake. "This is definitely a DNA case," he said. Kobilinsky said the markers found on the long johns are not enough of a profile to "match" those found in the panties, as Lacy wrote in her letter exonerating the Ramseys, but he would describe the markers from both the long johns and the panties as being "consistent" and noted that the DNA does belong to an unknown male. "Lacy did the right thing [in clearing the Ramsey family]," he said.

When questioned about hanging her hat on the DNA in her exoneration letter, Lacy said that she only did that because the DNA was "something tangible people could understand." The truth is, she said, she cleared the Ramseys not just based on the DNA, but also from looking at the totality of the evidence.

"There was no motive [for the parents], and no psychopathy," Lacy said. She added that she is one of only two people who have read the entire transcripts of Patsy Ramsey's psychiatric interviews, in which Lacy said she saw no indication of jealousy toward JonBenet or any violent tendencies. In 2006 when Patsy Ramsey was dying of cancer and even on her deathbed, Lacy said the distraught mother was trying to solve the death of her daughter.

Lacy, who was the Boulder County DA from 2001 until 2009, said the Boulder police investigation had ignored important evidence that pointed away from the Ramseys and instead focused on them while "trying to get the death penalty."

"They were running around the country looking for something negative on that family," Lacy said. But the Ramseys, she said, were clean.

The case is currently cold, but Boulder police say they are continuing to investigate any lead that comes in. It's recently attracted new attention this fall as the 20th anniversary of JonBenet's death approaches, and police have received hundreds of new tips.

A Lacy 'Apology Tour'

People who worked with Lacy remember her bringing John Ramsey into the Boulder County prosecutor's office around the time she exonerated the family. "She wanted us all to shake hands with him. We didn't know what to say ... it was like an apology tour," said one of Lacy's former DA investigators, Gordon Coombes.

Coombes, who worked in the Boulder prosecutor's office from 2008 to 2011, said he feels Lacy got too close to the family and lost her objectivity. "It was understood that if you didn't fall in line with the intruder theory, you were out," he said.

Another investigator who worked under Lacy, Ruth Aten-Shearwood, who is now a social worker in England, said that apart from a tight network of advisers, Lacy did not allow other investigators to work on the Ramsey case. Aten-Shearwood said she found out about the exoneration letter from watching the news. Said Aten-Shearwood, "I had to pick my jaw up off the floor."

Garnett, the current Boulder County DA, is running unopposed for his third term. Of Lacy's exoneration letter, he said, "This letter is not legally binding. It's a good-faith opinion and has no legal importance but the opinion of the person who had the job before I did, whom I respect."

When asked about the Ramseys, he said, "They, like everyone else, are presumed innocent. There's not enough admissible evidence beyond a reasonable doubt to charge anyone with this crime."

The Ramseys have always maintained their innocence. Burke Ramsey, now 29, recently filed a $150 million defamation suit against a forensic pathologist who claimed he was involved in the murder on CBS’ "The Case of: JonBenet Ramsey." Burke's attorney, Lin Wood, told ABC News that Burke was falsely accused of being responsible for the death of his sister.

Wood told ABC News he has tremendous respect for Lacy and the work she did during her time as DA. "This was a one-side, unfounded and brutal attack on Lacy who served well the citizens of Boulder for eight years," he said of the Daily Camera report.

Later, he added that he is encouraged that the DNA is being called into question because "now maybe all of those other suspects who were excluded will have to be reinvestigated."

Lacy told ABC News she stands by her decision to exonerate the Ramseys, insisting that "if the evidence had been there [to prosecute them], I'd have gone for it."