Former Cook County chief medical examiner Dr. Nancy Jones spoke at length for the first time since being forced from office in June, exclusively to the Sun-Times, and the picture she paints is not pretty.

Jones joined the office July 1, 1986, as part of a fellowship training program under the original medical examiner, Dr. Robert J. Stein. She worked for him and his successor, Dr. Edmund R. Donoghue. The environment had its challenges, she said, staffed with patronage workers, including drug addicts who could not be fired because they were close to the Stroger family. Going through the pockets of the deceased was routine.

“A lot of illusions I had about the office were shattered,” Jones said. “Under the former chief medical examiner, theft was pretty rampant. If something would disappear and someone would complain, Dr. Donoghue would say: ‘Call the attendant on duty, tell them to bring it back.’ But he wouldn’t discipline them. And it only happened if families complained. A lot of time the families don’t know what loved ones had on them when they passed away.”

Reached at his home in Georgia, Donoghue acknowledged that theft took place but insisted that he always disciplined people.

“It was not ignored,” he said. “I certainly had no firsthand knowledge of anyone who wasn’t disciplined, if we knew.”

As roundly criticized as former Cook County Board President Todd Stroger was, Jones, named chief medical examiner in July, 2007, found she could work with him.

“I was getting more help from President Stroger as far as cleaning up the office,” she said. “I know a lot of people didn’t like him, and he did appoint a lot of inappropriate people to inappropriate positions, and carried on the tradition ever since there’s been a county, though [under Stroger] it was a bit more blatant. The office was thought of as an 8th Ward dumping ground, for years, and it was. They figured, we can’t hurt anybody because they’re dead.”

But her ability to run her operations, she said, changed in 2010, when Toni Preckwinkle became Cook County board president.

“This woman is evil,” Jones said.

The two didn’t even meet for the first half year Preckwinkle was in office.

“Nobody ever introduced me,” Jones said. “I never met Toni Preckwinkle, nobody even introduced us for over six months. I was going to board meetings downtown, one day she walked past me, and I told Martha Martinez [a top Preckwinkle administrator], ‘You know, I’ve never met her.’ Martha said, ‘You’re kidding.’ ’’

When they finally did meet, it did not go well.

“It was at a pre-agenda meeting, when you have an item, you go and meet with the president. She started doing this face-washing gesture — rubbing her face over and over. I had the feeling I made her very uncomfortable — Neil, you and I met. I’m not a scary person. She kept doing it. I don’t think Toni Preckwinkle is comfortable discussing death and dying — a lot of people aren’t, but that was the first indication she was uncomfortable around me.”

Preckwinkle, in a statement, had only praise for Jones.

“As I’ve always said, Dr. Jones is an accomplished pathologist who has years of experience and expertise which she had dedicated to Cook County over her tenure here,” Preckwinkle wrote. “Given the concerns and longstanding issues that have been raised with this office, it is clear that new leadership was warranted to ensure the Office of the Medical Examiner more effectively and efficiently serves the residents, including those most in need, of Cook County.”

Jones said that budget cuts and politically motivated personnel shuffles led to the chaotic conditions at the Harrison Street office.

“We were told to cut our budget, and we foolishly did,” Jones said. “While a bunch of other departments refused, we did, though I said, ‘You cut my budget, we’re going to run into problems.’ It was cut anyway.”

Problems included services being cut off for non-payment.

“The medical examiner’s office was getting sued,” she said. “By suppliers, by people we had contracts with, because the comptroller’s office wasn’t paying them. We’d send bills downtown and they weren’t paying them. Lee Lumber sued us. Medical waste was building up because the company contracted to take it away wasn’t being paid. I wasn’t allowed to tell anyone this.”

They had tried to get more money in the budget.

“The way the economy was going, we knew more and more people weren’t going to be able to take care of burial or financial arrangements for their loved ones,” she said. “Even back in 2010, we knew we would have to increase certain parts of our budget.”

Instead, her staff was cut.

“It was Kimberly [Jackson] and I trying to do five people’s work. It’s impossible. You can’t.”

Jones said she tried to stop the practice of stealing from the dead — employees were suspended — but that left her open to criticism.

“I was always accused by black employees of being racist,” she said. “Any discipline I did, they always said it was because they were black.”

As far as the “House of Horrors” front page of the Sun-Times, she said that occurred while she was on vacation.

“Actually, a big part of that was staged,” she said. “My first notice that the cooler was in disarray was when Toni Preckwinkle’s press people called to say Mark Brown wants to come and see the cooler because he had heard it was more crowded than it ever had been. It was my first day back from vacation. I walked downstairs to see, walked in and almost . . . I was really ready to kill people. It was a disgrace.”

She pointed out that, the previous July, Gov. Pat Quinn had stopped the funding for public aid burials. “A lot of funeral directors continued to take remains, who would be buried under public aid, hoping the governor would realize the error of his ways and reinstate the funding for public aid burials.”

But eventually they gave up and started sending the bodies back to the morgue. “Instead of getting one or two storage cases a day, we were getting eight or 10 in a single day.”

Even then, she said, the bodies were handled “respectfully — nobody was on the floor, nobody was piled on anybody else.” Cleaning crews came every night.

“That’s why we know it was staged,” she said. “Just about anyone in the office will agree with that. It was made to look a lot worse than it really was.”

She speculates that employees being disciplined manufactured the scene in the night and turned the photos over to the newspaper.

“Whenever I go on vacation, they always had my cell number. I told them, in an emergency, call me. And they would call me for sillier things,” Jones said. “But when the cooler started getting full, nobody called me. All they had to do was pick up the phone.”

Jones pointed out that “for all the shenanigans that have been going on for decades,” most of the morgue technicians “are really caring and straightforward” though “some are thieves,” including one recently promoted who “bragged about filling his gas tank from loose change found in the pockets of the deceased.”

She said she is going public to set the record straight.

“I never got a chance to defend myself,” she said. “My reputation as a forensic pathologist is intact. What hurt was having to face my neighbors every day. The reason I’m doing this is because the [medical examiner’s] office was damaged by downtown. Instead of them taking responsibility, I and Kimberly [Jackson, former top executive adminstrator] ended up being sacrificial lambs.”

Does she accept any responsibility for what happened in her office? What was her role?

“Being stupid,” she said. “I am so apolitical. It was Commissioner [John] Fritchey who said, it’s not that I’m not a talented forensic pathologist, but that I’m not a politician. I took that as a compliment. There would be some things I would have done differently. I would have been a bit more insistent that my deputy chief assume responsibilities and do more of her job.”

On a more positive note Jones, whose blood pressure was sent soaring by the episode, is glad to be gone. She is happy, and has more time to ride the horses she loves. “I’ve never been so relaxed,” she said. “I feel like a new person.”