By the spring of 2009, Charles "Joe" Hynes was nearing the end of his fifth term of service as Brooklyn's District Attorney.

His reputation was mixed: His office had been dogged for a long time by charges of cronyism, and he'd recently been forced to drop charges in a high-profile murder conspiracy case against a former FBI agent when his key witness gave false testimony. But the onetime hero of the Howard Beach racial case had over his years as district attorney earned praise from criminal justice reform advocates who liked his progressive drug treatment and alternative sentencing programs.

And so Hynes, at the age of 74, decided that his accomplishments would outweigh his faults in the eyes of Brooklyn voters, and he'd run for a sixth term. The campaign was easy. No one ran against him.

But that easily gained sixth term proved to be so full of trouble and embarrassment that it could well tarnish his entire career.

• One of Hynes's most senior and trusted assistants, Michael Vecchione, was accused of railroading a Brooklyn murder suspect by withholding evidence and suborning perjury, prompting a $150 million lawsuit that has, often publicly, portrayed Hynes's office as a rogue operation in which misconduct was not only condoned, but encouraged.
• A homicide detective who had worked intimately with the office came under fire after Hynes agreed to vacate a 23-year-old murder conviction based on the detective's flawed work. Hynes ultimately wound up agreeing to review some 50 cases the detective had worked on with Brooklyn prosecutors to determine if others had been wrongly convicted and imprisoned.
• The New York Times produced a scathing series of stories about how his office gave favorable treatment to sex offenders in Brooklyn's politically influential Orthodox Jewish Community.
• The withholding of evidence in a botched rape case led to the resignation of two prosecutors in the office.

None of it was enough to discourage Hynes from, in 2013, running for a seventh term. But it seems it was enough for Brooklyn voters to remove him from office, as Hynes last fall became the first incumbent Brooklyn district attorney to lose at the polls in 102 years.

ProPublica spent 2013 examining questions of prosecutorial misconduct. We documented how infrequently prosecutors are punished for often serious misconduct. We looked in detail at the careers of two prosecutors, including Hynes's assistant, Vecchione, to illustrate how, even in the face of proven or alleged misconduct, prosecutors can nonetheless see their careers advance. We for the first time explored the potential abuse of the powerful prosecutorial tool known as material witness orders. And we took the most in-depth look at a current and potentially problematic prosecution: the murder case against a mentally ill man accused of killing EtanPatz, a 6-year-old when he went missing on his way to school in Manhattan in 1979.

Hynes's office was the focus of much of ProPublica's work. And while Hynes spends his final days in office, it is worth appreciating that the trouble that colored his sixth and final term in office is far from settled.

The $150 million lawsuit brought against Hynes and his office for the wrongful murder conviction of a man named Jabbar Collins could play out for months, even years. Collins's lawyer has accused Hynes of having over the course of many years knowingly failed to discipline troubled prosecutors in his office. He has accused Hynes of having run a "civil jail" in which witnesses were coerced into providing false testimony in criminal cases. He has accused Hynes of protecting Vecchione, the man who prosecuted Collins.

Hynes and Vecchione have publicly insisted they did nothing wrong, and consider the lawsuit to be without merit. But the lawyer, Joel Rudin, has conducted numerous and lengthy depositions with members of Hynes's staff, and has won access to once confidential office documents. Within the last two weeks, he has conducted a second round of questioning of Vecchione, and deposed Hynes for more than seven hours.

The investigation into the cases involving Louis Scarcella, the detective accused of strong-arming confessions, has been underway for months, but it is unclear whether it has identified any cases that need to be reconsidered. Certainly, there has been no announcement that anyone is being formally exonerated or freed from prison as a consequence of the investigation.  Hynes was criticized for appointing people who had been contributors to his campaigns over the years to the 12-member panel of lawyers and judges charged with overseeing the Scarcella probe.

Scarcella has insisted for months that he led an honorable career and never framed anyone across his more than two decades of work as a detective.

The future of the Conviction Integrity Unit Hynes had put in place years ago is also to be determined. The unit, meant to examine any legitimate challenges to convictions won by the office, was deep into at least one case when it abruptly lost its chief, John O'Mara.

The unit had been working in tandem with Anthony Mayol, a lawyer representing a man named Jonathan Fleming. Fleming is a Brooklyn man who is now serving his 23rd year in prison for a murder he says he didn't commit. Members of O'Mara's unit traveled to South Carolina along with Mayol's private investigators in November to interview a new witness. The witness told them that he drove the real shooter away from the scene of the crime, and it was not Fleming, according to Mayol.

Mayol also said O'Mara's unit found receipts showing that Fleming was paying his phone bill at a hotel in Florida just hours before the murder—information that was never disclosed to the defense at trial.

Mayol recounted to ProPublica a conversation he had with O'Mara on Dec. 12.  Mayol said he asked if it was a good time to talk. "He said, ‘Well, it's both a bad and good time because in one hour I'll be out of here. I'm packing my stuff.' He just punted it."

In an email to ProPublica, O'Mara said "the investigation is at a delicate stage and detailed discussion and publicity risks the integrity and possibly the outcome of the matter," adding that he met with the transition team for the incoming district attorney and gave them "detailed information about this and other ongoing cases."

Sorting through the array of issues left in the wake of Hynes's sixth term will fall to the borough's newly elected district attorney, Kenneth Thompson.

A spokesman for Thompson said that Thompson intends to add more prosecutors, investigators and paralegals to the Conviction Integrity Unit and that he'll "ensure a fully independent review of the dozens of cases involving Mr. Scarcella."