Early one morning last October, Chicago firefighters responding to a smoky 15-unit building at 79th and Greenwood made a gruesome discovery in a third-floor apartment that was burning: the decomposing body of a man.

Found under a pile of trash, the body bore no burns despite the fire, which was quickly determined to be suspicious.

An autopsy done hours later found “no clear evidence of trauma,” according to the pathologist, Dr. John E. Cavanaugh, who listed the cause and manner of death as “undetermined.”

Not an uncommon ruling when there are no obvious signs of how someone died. But, in this case, it was wrong, the Cook County medical examiner’s office now says.

The unidentified, African-American man had suffered multiple wounds from an assault, the office of Dr. Ponni Arunkumar, the chief medical examiner, told the Chicago Sun-Times.

The cause of death has since been changed to homicide. It’s one of several cases Cavanaugh mishandled in the 10 months he worked at the medical examiner’s office before being fired last Nov. 30, according to Arunkumar.

Now, Arunkumar’s office — which reports to Cook County Board President Toni Preckwinkle — is reviewing each of the 218 cases that Cavanaugh handled. They include two dozen deaths he ruled were homicides and 16 he determined were suicides.

Arunkumar calls the review unprecedented.

It could take months to complete. So far, nearly six months after Cavanaugh was fired, Arunkumar’s staff has finished reviewing just 23 of his cases, changing the cause or manner of death in eight of those.

Dr. Ponni Arunkumar, Cook County's chief medical examiner.

Dr. Ponni Arunkumar, Cook County’s chief medical examiner. | Ashlee Rezin / Sun-Times

Arunkumar hired Cavanaugh — a longtime pathologist for various counties in Indiana — to be her top deputy. Within six months, she demoted him, then fired him because she determined his “skill set” wasn’t right for one of the busiest morgues in the United States.

Arunkumar’s agency has notified Cook County prosecutors and the Chicago Police Department because findings of any mistakes by Cavanaugh could affect criminal investigations and prosecutions.

There’s also the emotional toll on families of the dead. Arunkumar says she and her staff have spoken with grieving relatives now faced with a new set of circumstances surrounding the death of a loved one.

The medical examiner’s office has touted improvements since revelations in 2012 — four years before Arunkumar assumed the top job — that corpses in blue body bags were being stacked in hallways as pathologists couldn’t keep pace and coolers overflowed with bodies.

In recent months, though, the Sun-Times has reported that some of the agency’s investigators, who help collect evidence for pathologists, have checkered pasts and faced disciplinary action for failing to visit even a single crime scene each month — the agency’s minimum standard and one that’s far less than required by state law and county ordinance.

The Sun-Times also has reported that the FBI believes Arunkumar’s office botched a murder case, incorrectly finding that Chicago police Sgt. Donald Markham shot himself in the head in 2015. Federal agents believe he was murdered.

Arunkumar stood by Dr. Steven White’s ruling that Markham committed suicide, rejecting the FBI’s assertion — based on an investigation that began with a tip and included a review by a pathologist who formerly worked for the Cook County agency — that White, an assistant medical examiner, was wrong.

But Arunkumar isn’t defending Cavanaugh, who worked for three coroner offices in Indiana before being hired as Arunkumar’s top deputy, a job he started in February 2017 at $250,000 a year.

“We have not had a situation like this,” Arunkumar says.

She credits her agency’s “peer-review” procedures for discovering problems with Cavanaugh’s work last October. A semi-annual audit of staff members found errors in “four or five” of six  Cavanaugh cases examined, according to Arunkumar. She says her office also will intensify its audits of autopsies and reports for all new pathologists.

“We have notified the state’s attorney . . . that any case done by Dr. Cavanaugh will involve another report with a second signature,” Arunkumar says.

Besides making exam-room mistakes, Arunkumar says Cavanaugh’s reports on death cases were rife with omissions and contradictions and that he sometimes failed to document “injuries” to the deceased.

She also says Cavanaugh took too long to wrap up his cases, 90 percent of which are supposed to be ruled on and closed within 90 days, ideally within 60 days.

How the office rules on a death — determining whether it’s from natural causes or a homicide or suicide or accident — can prompt a police investigation or mean there won’t be one.

The apartment building at 7940 S. Greenwood where a body was found last October of a man on whose body Dr. John E. Cavanaugh found “no clear evidence of trauma.” Later, the Cook County medical examiner's office changed that finding, saying the man had suffered multiple wounds from an assault and was a homicide victim.

The apartment building at 7940 S. Greenwood where a body was found last October of a man on whose body Dr. John E. Cavanaugh found “no clear evidence of trauma.” Later, the Cook County medical examiner’s office changed that finding, saying the man had suffered multiple wounds from an assault and was a homicide victim. | James Foster / Sun-Times

Besides failing to determine that the man found in the South Side fire was a homicide victim, Arunkumar’s staff found that Cavanaugh reached erroneous conclusions in cases involving:

• A 20-year-old man fatally shot last September at an apartment near 62nd and Artesian. Cavanaugh concluded the man shot himself in the head. Another Cook County pathologist, Dr. Adrienne Segovia, revised the manner of death to “undetermined” because another man had been seen with the handgun in the apartment and now can’t be found.

• A 2-year-old boy who collapsed in February 2017 at an apartment in the 1700 block of Juneway Terrace. Cavanaugh found the boy died from natural causes due to “anoxic encephalopathy with bilateral lobar pneumonia.’’ Segovia ruled the cause of death undetermined because there was “no clear cause for his abrupt collapse and extensive brain damage,” and there were “contradicting stories regarding who he was with at the time of his collapse.” She also noted that the boy had “unexplained bruising to the mid and left forehead, lateral to the left eye and on the abdomen” — marks that “are not expected in the course of routine resuscitation.”

Dr. John E. Cavanaugh ruled a 2-year-old boy who collapsed and died in February 2017 at an apartment in the 1700 block of Juneway Terrace died of natural causes — a finding his office later changed.

Dr. John E. Cavanaugh ruled a 2-year-old boy who collapsed and died in February 2017 at an apartment in the 1700 block of Juneway Terrace died of natural causes — a finding his office later changed. | Tyler Lariviere / Sun-Times

• A 58-year-old man who was found unresponsive sitting in a kitchen chair at his Skokie home last October. Cavanaugh listed the cause of death as “mixed medication toxicity” but ruled the manner of death was undetermined. Segovia changed that finding, saying it was a natural death, finding the man died from “hypertensive cardiovascular disease” following surgery for a herniated disc.

Arunkumar says the changed rulings aren’t just a difference of opinion, saying Cavanaugh’s work “did not meet our quality assurance standards.”

Arunkumar says it’s imperative “someone’s skill sets fit” with such “a busy office” and that she believed Cavanaugh’s did when she hired him.

Cavanaugh, 60, who lives in Crown Point, Indiana, works for the coroner’s office in Indianapolis — where Arunkumar had allowed him to work part-time during his time in Cook County. He estimates he’s handled 5,000 autopsies over a two-decade career as a pathologist.

Cavanaugh says the problems that led to his firing were “not so much over the autopsies as it’s the reports.” He says that was largely because he wasn’t used to the office’s computer system, which he says was glitchy.

He says he quickly realized the Cook County job wasn’t for him, as he had to deal with union issues involving outsourcing of the agency’s toxicology laboratory, for instance, and “a revolving door” with staff quitting.

“It was more of a culture thing,” Cavanaugh says. “I was out of my comfort zone.”

Of his demotion to a regular pathologist’s post after several months, which reduced his salary by nearly $22,000, he says “they didn’t so much demote me as I asked to be demoted” to get away from bureaucratic duties and get “back in the morgue and doing autopsies.”

A county spokeswoman says Cavanaugh “accepted a demotion” during a meeting to “discuss his job performance.”

Cavanaugh acknowledges being slower than required. “I’d go over the 90-day limit,” he says. “There’s really no excuse for that.”

The Cook County medical examiner’s office is reviewing each of the 218 cases that Dr. John E. Cavanaugh handled.

The Cook County medical examiner’s office is reviewing each of the 218 cases that Dr. John E. Cavanaugh handled. | Sun-Times files

According to records on Cavanaugh’s autopsy of the man found in the fire last October, he missed key wounds that showed the death was a homicide.

The man — his name is still a mystery — died from “multiple injuries due to an assault,” the medical examiner’s officer later determined, “amending” the finding so the case is designated a homicide and must be investigated by the Chicago police.

There were “sharp force” injuries to the “right lower neck/upper chest” and “right upper chest,” according to records that also show:

• A “possible sharp force injury” on the left side of the chest.

• “Possible blunt force” to the right side of the forehead and a wound near the left jaw and upper neck.

• “A slanting gaping sharp force wound with jagged margins.”

• And a “sharp force wound” on the man’s left palm.

Cavanaugh won’t discuss that or any other case. But he says ruling the cause and manner as “undetermined” is “leaving the door open” to a later, more decisive ruling, “it’s a placeholder.”

That’s not true, according to the county spokeswoman, who says such cases are supposed to be ruled “pending” and that an “undetermined” ruling means a pathologist couldn’t make a determination.

“Nobody’s perfect,” Cavanaugh says. “But I’ve got the bugs worked out — except for the computers.”

Arunkumar says she has reported Cavanaugh to the Illinois Department of Financial and Professional Regulation, which licenses and disciplines doctors. Officials there won’t say whether they’re investigating.

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