Jones was under fire almost immediately after a January report in the Sun-Times, which included complaints from morgue staffers about trays being full in the 300-capacity body cooler. That led to many of the deceased being stacked atop each other in blue plastic tarps against a wall. One staffer called the treatment of the dead “sacrilegious” and complained at the time that blood and other bodily fluids were pooling on the cooler floor creating an unbearable stench and a potential health hazard.

One of Jones deputies also is out the door. Kimberly Jackson, who as the morgue’s morgue executive officer was charged with planning indigent burials, was asked to step down.

Daryl Jackson — no relation — from the Illinois Department of Public Health has been tapped to take over her duties and a number of other administrative tasks, Preckwinkle said.

Preckwinkle said that in the five months since the problems were revealed, the M.E.’s office has worked to shore up operations, firing four staffers and filling vacancies.

An electronic case management system, funded with a $175,000 grant, is in place to keep track of when bodies arrive — and ensure burial arrangements are facilitated.

And the county’s Homeland Security Office is examining the facility to ensure it’s safe for employees.

“We have all kind of people that come to the medical examiner’s office and we want to make sure the staff is safe and that we have the correct cameras because there have been issues depending on the victim that’s there,” said Robin Kelly, Preckwinkle’s Chief Administrative Officer, who is overseeing the M.E.’s office.

“I think there are leadership issues which we’ve worked hard over the last six months to address – leadership and staffing issues,” Preckwinkle said.

Jones’ exit had been expected for months.

In January when the problems first became public, Preckwinkle said that management of the morgue was part of the problem and hinted at the time she’d like to show Jones the door.

“There have been recurring problems there, that’s quite true,” Preckwinkle told reporters in then, referring to the morgue. “My ability to deal with it is limited by the fact that the person who is in charge of it has a term of office as opposed to serving at my pleasure.”

She meant that Jones — who was serving an open-ended term of office — wasn’t a political appointee who Preckwinkle could discipline or fire.

Following the Sun-Times and, later, other news reports, Preckwinkle dispatched her deputies from downtown to the facility at 2121 W. Harrison to eyeball operations. The county’s independent inspector general launched a probe, as did the state’s labor department, fraying nerves among morgue staff who declined to give their names when commenting to the paper out fear they’d be targeted.

According to morgue staff — some sympathetic toward Jones, others not — say they witnessed Jones walking around the office and talking openly about how she expected to be axed.

In January, Jones responded to the Sun-Times questions about the crowded cooler — saying the pileup of bodies was the result of cuts to state aid that covered the costs of burying the poor. She also said a backup of fetus burials was a result of a change in county ordinance. In 2011, critics raised questions about the remains of babies and fetuses — many who had died at birth or as a result of miscarriage — being combined for burial. So county commissioners changed the ordinance requiring the remains of babies and fetuses be placed in separate compartments. And, Jones said in January, they were awaiting special burial boxes.

And while she said the cooler was at capacity, she denied the numbers her own staff provided the Sun-Times: Roughly 400 adults and about 100 babies or fetuses. Days later, the Preckwinkle administration said there were 363 bodies in the cooler.

On Tuesday, officials said there were 234 adults and 56 fetal remains in the cooler as of June 2.

Throughout the controversy, Jones declined to take reporters calls and or answer questions about the morgue. At one point she told a Sun-Times reporter she wasn’t allowed to speak to the media and that all questions had to be directed to Preckwinkle or one of the board president’s spokespeople.