The three-hour flight from Los Angeles landed shortly after 5 p.m. at the Jefferson County airport, a few miles from the upscale Boulder home where JonBenet's father discovered her body on the day after Christmas 1996. Karr, in handcuffs both as he entered and exited the plane, was put into a black sport utility vehicle and driven away in a convoy, with news helicopters trailing overhead.
The plane ride offered none of the prawns, wine and champagne that accompanied Karr's Thailand-to-California flight, but the former schoolteacher was allowed to wear dark slacks and a red shirt instead of a prison jumpsuit.
The convoy was to take Karr to the Boulder jail, where he's likely to be separated from the jail's general population and held until his first court appearance, CBS News' Jennifer Miller reports.
"Anybody that's in jail in our population that faces these kinds of charges, charges against children, faces some danger," Boulder County Sheriff Joe Pelle said.
Karr's arrival in Boulder comes as a former landlord claims that when Karr was renting a room from him in Costa Rica, Karr bragged that he was sexually "like a wolf," and said he "liked little boys and girls."
"I had to kick him out because he was obviously a pervert and I was worried about the safety of my wife and my stepdaughters," said the former landlord, Canadian John Hall.
Meanwhile, in Boulder, the county public defenders' office has asked to meet with Karr, who has not been formally charged. His first court appearance in Boulder will probably be announced Friday, according to the district attorney's office.
During an initial hearing, judges advise defendants of their rights to remain silent, to have an attorney and to post bail unless it's denied. A preliminary hearing must be scheduled within 30 days after formal charges are filed.
Questions about Karr's involvement in the case have arisen since he told reporters following his arrest in Thailand last week how he was with the 6-year-old beauty queen at the time of her 1996 death but that it was an accident.
Boulder County prosecutors have refused to detail any evidence they might have, but in a court filing this week said investigators didn't learn of Karr's name until Aug. 11, five days before his arrest in Thailand. They said he was arrested in part because they feared he might get tipped off and vanish.
"It is like this guy fell out of the sky for them and they're trying to figure out what they have going," said Laurie Levenson, a professor at Loyola Law School and a former federal prosecutor. "They can't really let him go or proceed to convict him until they have the evidence. It's in a bit of a limbo now."
The court filing conflicts with the Sonoma County, Calif., sheriff, who said his office alerted Boulder authorities about Karr in 2001 after he was arrested on child pornography charges. The sheriff and Boulder prosecutors both declined to comment on the apparent discrepancy.
Karr, 41, has professed love for JonBenet in e-mails with a Colorado professor, and told a California woman, Wendy Hutchens, he believes the little girl was tortured before she was strangled.
Sonoma County sheriff's Lt. Dave Edmonds said Karr expressed an "apparent fascination" with the 1993 murder victim Polly Klaas and JonBenet, and "presented ideas about what the murderers of Polly Klaas and JonBenet Ramsey must have thought and felt." But there was no confession, Edmonds said, or anything else to suggest Karr played a role in JonBenet's slaying.
The Boulder arrest warrant and supporting affidavit remain sealed and the district attorney is fighting media requests to open them. Prosecutors said in Wednesday's court filing that the affidavit contains evidence never before disclosed publicly.
"To a large extent, the evidence from the investigation in the affidavit has to do with Mr. Karr and it was only developed recently," wrote Bill Nagel, an assistant district attorney. "Furthermore, the investigation of Mr. Karr is in its very early stages."
After JonBenet's father, John Ramsey, found her body in the family's basement on Dec. 26, 1996, police collected DNA from blood spots in her underwear and from under her fingernails.
Investigators have said some of the DNA was too degraded to use as evidence, but some was of sufficient quality to submit to the FBI in 2003. The sample did not match any of the 1.5 million samples in the agency's database, according to the Ramsey family attorney.
Other evidence includes the ransom note, a mysterious boot print found outside the house, marks on JonBenet's body that some say could have been made by a stun gun; and signs that someone may have entered the house through a basement window.
Karr was arrested in Bangkok last week and flown over the weekend to Los Angeles, where he decided not to fight extradition to Colorado on a warrant listing charges of murder, kidnapping and sexual assault on a child in JonBenet's 1996 slaying.
Karr's family contends he was with them in Georgia at the time of the Colorado killing, while an ex-wife has said she believes Karr was likely with her in Alabama. Neither she nor the family has offered definitive proof.
Dozens of attorneys have come forward offering to represent Karr, who does not yet have a legal team in Colorado. Defense lawyers say early hearings in the case are mostly perfunctory and it would probably be better for Karr to have a public defender in Boulder at first.
"It would probably be helpful for him to have an adviser on that who is not the one who will eventually take the case, someone who has his best interests at heart who doesn't have an economic motive," said Los Angeles attorney Gloria Allred. "The truth is, a lot of people don't have that luxury."