In July, The Times published an investigation detailing 129 cases of inmates who had been seriously injured during encounters with correction officers over an 11-month span last year. Less than a month later, the United States attorney in Manhattan, Preet Bharara, threatened to sue the city after releasing a report that accused the Correction Department of failing to protect adolescent inmates from excessive force by guards.

Mr. de Blasio vowed last month to overhaul the department, which he called the city’s most troubled agency, and to bring an end to the violence at Rikers. He has entrusted the task to his handpicked correction commissioner, Joseph Ponte, who has a national reputation as a reformer. Their single biggest challenge may well be reining in Mr. Seabrook, who has outmaneuvered a long line of mayors and commissioners over the years.

Staunch Adversary Is Ousted

During her four years as the deputy commissioner for investigation, Ms. Finkle was an awkward fit at the Correction Department. In part, it was because her position, investigating wrongdoing, put her at odds with the uniformed staff. But it was also because of her background and personality.

In a heavily minority organization that is largely blue collar and defined by its macho culture, Ms. Finkle is white, a graduate of an elite college and openly gay. She also had little patience for the niceties needed to negotiate the department’s politics.

When she refused to fall in line with Mr. Seabrook, he accused her of having it in for his members. “Flo Finkle had her own agenda,” he said in an interview. “She just wanted to kill people.”

Before she joined the department in 2010, Ms. Finkle had spent roughly two decades investigating misconduct by the police, including serving as executive director of the Civilian Complaint Review Board, which provides oversight for the Police Department. While at the Manhattan district attorney’s office in the 1990s, she sent three officers from the 30th Precinct in Harlem to prison as a prosecutor in what became known as the Dirty Thirty case, one of the biggest police corruption investigations in recent history.

Before Ms. Finkle’s arrival, brutality cases at Rikers had usually been handled as internal disciplinary matters. But at the June 2012 meeting, which she conducted with a member of the city’s Department of Investigation, Ms. Finkle announced a major shift, warning that more officers who brutalized inmates would face criminal prosecution, according to two former investigators and a midlevel uniformed officer. And, she said, even cases that involved lying to investigators or falsifying incident reports would be punished as felonies, and could land officers in prison.