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In the middle of New York City, they had been cut off from the world.

It was the end of January, and hundreds of inmates at the Metropolitan Detention Center in Brooklyn had been locked in their cells after an electrical fire knocked out power in the building. There, it turned out, they would spend the coldest days of the winter in darkness, largely without heat and hot water.

“It’s cold as hell,” one inmate, Sean Daughtry, told his lawyer. He could see his breath in the weak light that slanted through his cell window.

When news of how the inmates were treated reached the world outside, the warden of the federal jail, Herman E. Quay, at first denied there was any problem outside a partial loss of power. “Inmate housing units have been minimally impacted,” Mr. Quay’s office told The New York Times during the blackout, a message initially echoed by the Bureau of Prisons in Washington.

But dozens of interviews with inmates and their families, defense lawyers, jail staff, union officials and lawmakers briefed on the response of officials at the Bureau of Prisons painted another picture, revealing an account of the crisis that not only contradicted what the bureau said, but suggested it was even worse than it had initially appeared.

The blackout, which lasted for a week, ended Feb. 3, when power was restored amid public outcry. A few days later, the Justice Department, which oversees the federal Bureau of Prisons, said that it was “committed to the safe and humane living and working conditions of all inmates and employees,” and that its internal watchdog, the Office of the Inspector General, would investigate the facility’s infrastructure and emergency response.

Mr. Quay did not respond to requests for comment.

The blackout crisis was just the latest episode in a long history of neglect and brutality at the jail, one that has been documented in previous Justice Department reports. Investigators over the years have issued findings that suggest the jail is among the worst in the federal system, determining at different times that prisoners have been beaten, raped or held in inhumane conditions.

“It’s my opinion,” a former warden at the jail, Cameron Lindsay, said in an interview, that over the last decade “the M.D.C. was one of the most troubled, if not the most troubled facility in the Bureau of Prisons.”

The M.D.C., one of the largest federal lockups in the country, houses more than 1,600 inmates, some of them linked to high-profile drug trafficking and terrorism cases, most charged with lesser crimes. It is largely a way station, where inmates spend relatively short periods awaiting trial or sentencing.

While many federal inmates are held in less populous corners of the country, the M.D.C. sits between an expressway and the New York Harbor, amid one of the world’s great concentrations of lawyers and civil liberties advocates. Yet the jail has proved steadily resistant to attempts at scrutiny, including while under Mr. Quay.

After Representative Jerrold Nadler, a New York Democrat who heads the House Judiciary Committee, toured the jail during the blackout, he denounced not only the deplorable conditions, but “an absolute lack of urgency or caring by the leadership, particularly the warden.”

“Something weird is going on,” an inmate, Kaemar Wilson, said to his fiancée in a message in mid-January. “I’m frustrated. I can’t figure it out, but nothing is working properly.”

When his fiancée, Moriam Johnson, visited him a few days later, Mr. Wilson said the heating system and electricity seemed to be broken, but inmates were not given any explanation for the issues — or for the dinner of undercooked oatmeal the night before.

Around Martin Luther King’s Birthday, when temperatures plunged into the single digits, Mr. Wilson told his fiancée that the building felt like a freezer. To keep their hands warm, inmates on his floor had filled a can with water, heated it with a contraband lighter and passed it around.

Families began to call the jail. Union officials also called the warden. Anthony Sanon, head of the local chapter of the correction officers union, described workers in coats and gloves trying to keep order in the cold. “It was just unbearable,” he said.

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“The inmates were very agitated, very angry,” said Anthony Sanon, the head of the local chapter of the correction officers union. “They banged on the doors and cursed.”CreditYana Paskova for The New York Times

Mr. Sanon alerted regional union leaders. The warden and his staff assured him they would monitor the heat. “They were trying to sugarcoat it,” Mr. Sanon said. But the next weekend, on Jan. 27, a faltering electrical panel exploded, he said.

Another inmate, Donnell Murray, would later recall in a message to his fiancée, “The fire alarm was sounding off and I could smell the smoke, and we were immediately locked in our cells.”

Then, the jail went quiet.

The Bureau of Prisons said Mr. Quay adequately notified Washington about the “initial fire and subsequent events.” The bureau did not say when this was done and what it did in response.

Many inmates said that after the fire, the lights went out and they were locked in their cells for up to 23 hours a day, a lockdown typically enforced in emergencies, to keep staff safe. Asked how many days he was locked in, an inmate on the fourth floor later said he believed three consecutive days passed before he was released again, but he had become confused in his dark cell.

“I had no idea what time, what day — you lost track of everything,” the man, who asked that his name not be used for fear of reprisals, said in a phone interview.

Cold air blew from a vent over his bunk. He tried to block it with a book cover. He lay listening to a battery-powered radio, wrapped up in three blankets, he said, until a guard saw he had an extra blanket and took it away.

Still, he worried more about his cellmate, who suffers seizures and was not given his usual medication. The jail’s computers, used to request prescription refills, were down, along with the monitored phone system inmates use to call family. A line that connects the jail to local federal defenders’ offices was working, though, and when they were briefly released, the inmates began to call the lawyers.

“They sound really frightened,” said Deirdre von Dornum, who leads the Brooklyn office of the federal defenders, on Jan. 31. She said the number of calls peaked that day, when temperatures fell to 2 degrees.

The lawyers asked the warden to move the inmates or bring in blankets, but said they received only dismissive replies.

On Feb. 1, after news of the blackout broke, Ms. von Dornum obtained a court order to enter the jail. She found the building illuminated by dim emergency lights. The cells were pitch-black. The fetid smell of nonworking toilets pervaded the jail. Men pounded on cell doors.

In common areas, the temperature was bearable, but as she approached cells that faced the waterfront on one floor, she said, she was hit by a gust of cold air.

The jail staff would not open the cells, but through the cracks of doors Ms. von Dornum glimpsed the silhouettes of the men inside. “They were wrapped in everything they had, and they had tried to cover the windows.”

Inmates complained to her of the cold, brackish water that ran from the taps. A client known to swallow razor blades said he had not gotten his psychiatric drugs. In another cell, a man lay on bloody sheets.

The man, Sean Daughtry, had a chronic sore on his leg that had festered during the blackout.

“He had a raging infection,” his lawyer, Gary G. Becker, said later, after Mr. Daughtry was removed to a hospital. Mr. Daughtry, who was being held on charges of violating supervised release, said he had been denied antibiotics and Tylenol by jail staff. He was told to wash the wound with soap and water.

Union leaders, however, said M.D.C. staff “actually held it together” through the crisis. During the long week when the jail remained in perpetual twilight, correction officers worked late preparing makeshift meals — sandwiches, cereal — that they took from cell to cell, said Mr. Sanon.

“The inmates were very agitated, very angry,” he added. “They banged on the doors and cursed.”

On a floor that houses lower-security inmates, a man who gave only his first name, Michael, told his wife that a correction officer had at one point opened his cell door, allowing him into the warmer common area.

“I don’t know what’s going on here,” the guard had told him, “But this is inhumane.”

Mr. Quay began working for the Bureau of Prisons in 1995 and had previously been the warden at the federal prison in Danbury, Conn., according to court filings and his LinkedIn profile.

Protesters gathered outside the M.D.C., which is one of the largest federal lockups in the country. The warden of the jail, Herman E. Quay, at first denied there was any problem outside a minor loss of power.CreditStephen Speranza for The New York Times

Aimee Jamison, who was a case worker at McCreary, a federal prison in Kentucky, while Mr. Quay was an associate warden there, described him as a conscientious manager.

”He’s a straight-up guy, and he’s not going to go to overlook the health and welfare of anyone, inmates or staff,” Ms. Jamison said.

She said that Bureau of Prisons employees are used to working in circumstances that others might consider crises. “The bureau looks at things in its own way,” she said. “No matter what happens on the outside, we still go to work, and our job is to contain the inmates, no matter what.”

Still, Mr. Quay’s response to the problems this winter faced criticism from elected officials and others.

Mr. Lindsay, the warden at M.D.C. from 2007 to 2009, said every detention facility should have an emergency plan to deal with exigencies ranging from a missing tool to an escape to problems with heating. At the very least, he said, there should have been extra blankets.

“If this is accurate — where they haven’t had heat for days on end — in 20 years in the B.O.P. I never saw anything like that,” said Mr. Lindsay, who now works as an expert witness.

A facilities manager later testified at a hearing in federal court that issues began a week or two before the fire. The heating problems appeared to be at least partly unrelated to the electrical ones: on Jan. 21, some heating coils that draw water from the boilers had frozen in a cold snap and broke.

After the fire, Mr. Quay failed to set up an emergency command center or give staff instructions other than to keep inmates locked up, union officials said in interviews.

During the episode, which drew national attention to the treatment of inmates in federal jails, lawmakers demanded more answers from officials. Last week, many applauded when the Justice Department announced that its inspector general would investigate.

But some question whether that will be enough to change the culture of a jail that has now been accused of widespread mistreatment of prisoners for the third time in less than 20 years.

After the 2001 terrorist attacks, the inspector general found that officers slammed Muslim inmates face-first against walls and told them they would die in secret. The inspector general also participated in an investigation into the beatings of two inmates by officers in 2002 and 2006.

More recently, an investigation focused on officers who sexually assaulted female inmates who were on overnight cleaning duty between 2013 and 2016. Two former M.D.C. lieutenants and a correction officer were convicted, including one lieutenant who repeatedly raped a prisoner and threatened to send her to solitary confinement if she reported it.

Last year, another inspector general report condemned conditions for women housed in an adjacent building. The women were confined to one floor with almost no natural light or time outside.

Lawyers with the federal defenders, which represents hundreds of inmates at the jail, filed a lawsuit on Monday asking a Brooklyn federal judge to appoint an outside monitor who would have unfettered access to the jail.

“The I.G. previously has investigated M.D.C. and issued harshly critical reports,” said Ms. von Dornum, the federal defender. “But nothing has changed.”

In court papers, lawyers for the Bureau of Prisons argued the lawsuit applies only to a handful of inmates who allegedly suffered during the blackout. Those limited complaints cannot be the basis for the appointment of a monitor, they said.

Besides, the government lawyers wrote, the problems have been fixed.

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