Dr. Jones will remain as the medical examiner until the end of July. The county has launched a nationwide search for her replacement.
Serious management problems in the past six months at the morgue-- exposed by the ABC7 I-Team-- have put tremendous pressure on county officials to fix the floor to ceiling problems, starting at the top.
Cook County Board President Toni Preckwinkle announced Jones was stepping down on Tuesday.
Jones is considered a superb forensic pathologist by her colleagues, but also a weak administrator, according to current and former employees. When photos of bodies stacked up at the morgue surfaced in January, it was the beginning of the end for Jones. The pictures, taken by staffers, showed mishandled bodies left open to the elements, stacked on floors and crammed into coolers.
"We loved our brother. We loved him. What we went through I wouldn't want nobody to go through the same thing: wondering where there brother is. He's laying somewhere and nobody tells us," Bernice Terry said on January 25, 2012, of his brother, whose body was missing at the morgue.
Jones also became the new focus of an old - and criticized - practice: the burial of indigent bodies in mass graves. For weeks the public relations wounds festered.
"From very early on in our review of operations there, we believed that we needed stronger management," Preckwinkle said.
Even though Jones was the top manager of the morgue, Preckwinkle praised the doctor's 26 years of service and would not place blame on her for the morgue fiasco.
Jones, who has ducked ABC7's cameras and requests to answer questions for the past five months, did not respond Tuesday. She was not at the news conference.
County officials say there will be a nationwide search for her replacement. Preckwinkle, who replaced the hapless Todd Stroger, says Cook County's reputation won't be an obstacle.
"You know, I wanted this job despite the bad publicity that went on prior to my tenure. So I think there are probably other people out there who would want to take on the challenge," Preckwinkle said.
Whoever becomes the chief medical examiner for Cook County will get some fresh help on the administrative side. The county has hired a new executive officer to oversee the business side of the office, including indigent burials.
Preckwinkle says the current executive officer Kimberly Jackson was asked to resign, four other employees were fired, and eight were disciplined as part of the overhaul.