As the new year approached, the O’Connell investigation had followed an increasingly tangled path. It fell to the special prosecutor, Brad King, a longtime state attorney from a nearby district, to assess the two opposing scenarios of how Michelle O’Connell had died.

In March 2012, Mr. King’s office contacted the O’Connells and said he and his team would deliver his decision at the St. Augustine courthouse.

Everyone sat around a long table, and as Mr. King made his opening remarks, Ms. O’Connell’s mother grew impatient.

“They were beating around the bush, just giving real vague descriptions of what was going on, and she says, ‘Are you going to prosecute Jeremy Banks for the death of my daughter or not?’ ” recalled Michelle’s sister Jennifer. “And he said, ‘No, ma’am.’ ”

“The day my family met with Brad King I refer to as the second-worst day of my life,” the other sister, Christine, said. “Losing my sister was the worst.” Scott, the brother who worked as a deputy for Sheriff Shoar, unleashed a tirade so emotionally charged that it cost him his job.

Dominick Pape, the head of the state law enforcement agency’s Jacksonville office, was so unhappy that he called for a special inquest.

According to a five-page memo from Mr. King’s office, the decision had been based primarily on the pathologists’ findings. “Three medical examiners have reviewed the file and concluded that this was a suicide,” it states. To Mr. Pape, their conclusions — particularly Dr. Bulic’s upside-down-gun theory — were confusing and unpersuasive.

Dr. Hobin, the original pathologist, would ultimately change his finding three times. After saying it was suicide and then homicide, he told a local reporter he did not know what had happened, before telling The Times that he again believed it was suicide.

Mr. King had also asked a former medical examiner in his district, Dr. Steven Cogswell, to review the case.

As a military pathologist in the mid-1990s, Dr. Cogswell had been criticized for concluding that Commerce Secretary Ron Brown had been shot in the head before his plane crashed in Croatia, killing all aboard. Air Force officials categorically rejected his finding.

Asked about the O’Connell case in an interview, Dr. Cogswell said he could not recall it in detail.

Mr. Pape also complained that Dr. Bulic and Dr. Cogswell had not written reports explaining their decisions. Dr. Bulic said he had not done so because the case was actually Dr. Hobin’s, not his. He said he had looked into the case “out of my pure curiosity and to satisfy the many different people who came and asked about my opinion.”

As for Dr. Cogswell, Mr. King said, “I simply was not willing to spend 5,000 taxpayer dollars to get another report to say it’s suicide.”

The crime scene reconstructionist hired by the state agency, Jerry Findley, also took issue with the special prosecutor.

When Mr. King’s investigators came to talk to him, Mr. Findley said, “the whole tone of the interview was for me to tailor my report or soften my report to where it would be more conducive to suicide rather than homicide.”

In the prosecutor’s memo, investigators wrote that Mr. Findley had not considered the upside-down-gun theory.

“That’s a lie,” Mr. Findley said. “I did consider that, and like I told them, I ruled it out fairly fast,” because guns recoil after firing and the shells would have ejected in the opposite direction from where they were found.

That was affirmed in several tests conducted by Mr. Diaczuk.

Mr. King backs his investigators. “It’s not in his report that he ever test-fired the gun upside down,” he said in an interview. “You can’t predict necessarily where a shot shell is going to end up. You simply can’t.”

He also disputed firearms experts’ statements about the tactical light and the eye wound. “The recoil is essentially going to make the tactical light move forward into the face as opposed to away,” said the prosecutor, a former deputy sheriff. “That is also consistent with my years of training with firearms.”

For all that, Mr. King never explicitly stated that Ms. O’Connell had killed herself. He simply concluded that there was not sufficient evidence to bring charges.

The memo explaining his decision said that while the two witnesses who heard shouts and gunfire that night appeared credible, their testimony did not “support any type of homicide conviction on its own.”

In the interview with The Times, Mr. King said that looking at the evidence, “I think even you have to say it’s legitimately possible that she killed herself. And if that’s the case, I lose.”

In the end, he rejected the call for an inquest.

The Sheriff Reacts

Sheriff Shoar greeted the decision with gushing praise for Mr. King’s two investigators, Bill Gladson and John Tilley. In a letter to Mr. King, the sheriff described them as “class acts” and “on top of their game,” adding, “From one elected official to another, I would never try to recruit someone away from your office, but I did tell Bill and John that I may know of some decent real-estate deals in St. Johns County, just kidding of course.”

Sheriff David B. Shoar has admitted some flaws in his office’s investigation of Ms. O’Connell’s death, but he defends the conclusion that it was a suicide.

Kidding aside, with his political connections, ties to the business community and charming yet combative appeal, Sheriff Shoar was usually in a position to assert his will around the county.

“You’re talking about a tremendous amount of leverage that one man can wield in a Southern county, when you’re a sheriff,” said Ben Rich, a former law enforcement officer who served as the chairman of the county commission.

After starting as a St. Augustine police officer in 1981, Sheriff Shoar has been elected three times, twice unopposed. Challenging his authority is not without risk, Mr. Rich said.

“I confronted Sheriff Shoar in 2006 and 2007 when I was the chairman regarding his budget and the bloating of his budget,” Mr. Rich said, “and he declared war on me.” Mr. Rich was up for re-election at the time, and soon the sheriff began appearing in ads praising the experience of his 24-year-old opponent. Mr. Rich lost.

His hard edge notwithstanding, the sheriff has cultivated a somewhat eclectic persona. He is a leading member of an influential Christian prayer group that believes in spreading its gospel in government offices and schools. Well-versed in history and popular music, he is given to extemporaneous discourses that touch on the likes of Seneca and the Stoics, Keats, Shakespeare, Solzhenitsyn and Stonewall Jackson.

When Mr. King decided not to prosecute Jeremy Banks, the sheriff saw it as vindication. Case closed.

A year later, after The Times began asking questions, he went on the offensive. He began a new inquiry — into how the state agency had investigated the shooting.

Citing The Times’s interest in the case, the sheriff had his office spend “hundreds of hours” combing through interviews conducted by Mr. Rodgers and his direct superior, Mark Brutnell.

In late March, Sheriff Shoar released a report that accused Mr. Rodgers of hyping his case against Mr. Banks, coaching witnesses and using false information to get a search warrant. The report, given to the news media and law enforcement officials, also accused Mr. Pape of failing to rein in his agent.

Sheriff Shoar also paid two former law enforcement officers — one of them an acquaintance — to review his report, and both agreed that Mr. Rodgers’s investigation had been flawed. Neither examined the underlying evidence or conducted independent interviews.

The sheriff’s report, filled with opinion and at times factually inaccurate, also sought to discredit the testimony of Mr. Banks’s two neighbors, who had given sworn statements about hearing a woman screaming for help.

One of them, Stacey Boswell, said in an interview that Mr. Rodgers had never sought to influence their testimony. “He just asked us what we seen, what we heard that night,” she said.

The report also said the women had confessed to investigators for the prosecutor’s office that they often smoked marijuana together in the evenings and could not remember if they had done so that night. The statement was underlined, in boldface type.

But in the interview, Ms. Boswell said, “That’s not true.” And Leanna Freeman, the lawyer for the second neighbor, said one of the investigators, Robert Hardwick, had confirmed that the women made no such admission.

Ms. Freeman said she asked Sheriff Shoar to correct his mistake, but he refused. (Mr. Hardwick declined to be interviewed.)

In his report, Sheriff Shoar did finally acknowledge — briefly — his department’s failure to canvass neighbors, interview the O’Connells, download Mr. Banks’s cellphone data, isolate and photograph Mr. Banks, collect all his clothing, send evidence for testing, interview the paramedics, write a crime scene log and file the proper reports.

The sheriff also questioned the decision to assign two “relatively inexperienced” detectives to “such a sensitive case.” (Just two months after the shooting, one of those detectives, Mr. Tolbert, was reprimanded for sexually harassing a female officer, records show.)

Despite the mistakes enumerated by the sheriff, only two midlevel supervisors were disciplined, and not seriously.

A Light Touch

Sheriff Shoar describes himself as a disciplinarian. “I have terminated, demoted, suspended and reprimanded many subordinates over the years,” he wrote in his letter to The Times.

At times, though, he has shown a light touch with wayward officers.

Three years before the O’Connell shooting, the sheriff’s office broke up a peaceful graduation party in a predominantly black neighborhood, firing pepper gas, unleashing a police dog, brandishing shotguns and making nine arrests. “If I didn’t know better, I would have thought it was back in the ’60s — the only thing that was missing was a water hose,” said the party’s host, Charlie Gilliam.

Officers later filed a report saying that they were responding to a noise complaint, that they saw open bottles of alcohol, that bottles were thrown at them, and that the dog was unleashed after a young man pushed an officer.

But after internal affairs investigators determined that much of the report was fallacious, prosecutors dropped the charges, and residents received a $275,000 settlement. Sheriff Shoar, however, overruled his internal affairs department’s recommendation that the lieutenant in charge be suspended for three days and that an overly aggressive deputy with a history of misconduct be fired. In the following months, that deputy repeatedly engaged in misconduct before being dismissed.

As for the lieutenant, he would be the district commander on the scene the night Michelle O’Connell died.

A year before that, Sheriff Shoar’s disciplinary posture had been called into question in a domestic violence case involving a deputy named Halford (Bubba) Harris II.

Two supervisors learned of accusations that Mr. Harris had abused his wife. But no investigation was immediately opened, records show.

One sergeant did prepare an affidavit documenting the accusations. But he was told by his supervisor to hold it back, so he stuck it under the visor in his squad car, where it remained, even after another officer became aware of further incidents, according to Mr. Harris’s internal affairs file.

The case came to a head on Christmas Eve, when his wife fled their house and called the police. Internal affairs officers uncovered other possible acts of domestic violence before his hiring, records show. His wife said that before they married, he had held a knife to her throat and hit her. His ex-wife said he had threatened her with a gun. No charges were filed.

Col. Todd R. Thompson, the sheriff’s director of law enforcement, recommended that Mr. Harris be fired, saying his actions were “particularly egregious and trouble me deeply.”

In an interview, Mr. Harris insisted that he had never engaged in domestic abuse: “Is there proof?”

“They’re telling one story,” he added. “I’ll tell you another one.” He said the state attorney brought no charges and noted that, though they divorced after the Christmas Eve incident, his wife later wrote a letter of support, calling him “a wonderful man and father.”

Sheriff Shoar overruled the dismissal recommendation, citing mitigating factors, like an “exemplary” work record and an absence of citizen complaints.

“I hope you understand how fortunate you are to receive a second chance,” the sheriff wrote to his deputy.

After the decision leaked out and caused an uproar, Mr. Harris said, he was pressured to resign. He is now a deputy in a nearby county.