In his first week as New York City’s interim police commissioner, Thomas G. Donlon responded to a police shooting that injured four people, including one of his own officers.
He then had to prepare for the U.N. General Assembly, an annual logistical and security challenge that was compounded by deepening conflicts in Gaza, Lebanon and Ukraine.
On Friday, trouble came for the commissioner himself: Federal agents arrived at the residences of Mr. Donlon, 71, a former F.B.I. counterterrorism official hired after his predecessor departed amid an investigation. They seized documents that he said had come into his possession about 20 years ago.
According to two federal officials with knowledge of the matter, the materials that the agents sought were classified documents.
For a department and a city roiled by report after report of search warrants, resignations, subpoenas and investigations by prosecutors in the Southern District of New York, this latest development took a turn into the absurd.
“At a certain point, we all would walk out of the movie theater because the script was just too fantastical, incredulous, and unbelievable for real-life,” Jumaane Williams, the city’s public advocate, said in a social media post.
Others expressed dismay that yet another member of Mayor Eric Adams’s administration was under federal scrutiny.
“If this mayor cannot manage to appoint someone who is not immediately at risk of being raided by the F.B.I., then he should resign,” said Emily Gallagher, a Democratic state assemblywoman from Brooklyn who was among the first state lawmakers to call for Mr. Adams’s resignation this month. “We’ve got a lot of problems that need immediate attention and they’re not getting that because of all of these follies.”
Jessica Ramos, a Democratic state senator from Queens who recently entered the mayor’s race, said it was “impossible not to have questions about corruption and mismanagement” amid the turmoil. “Every investigation, every subpoena, every indictment is a slap in the face to New Yorkers who want to trust that their government is being led by good people.”
Mr. Adams appears to be the only mayor to have had three police commissioners during a single term since Mayor James J. Walker, who resigned in 1932 while being investigated for corruption. Keechant Sewell, the first woman to lead the department, left last summer after only 18 months on the job. Edward A. Caban, the first Latino police commissioner, resigned this month after federal authorities obtained a warrant to search his cellphone.
Then, Mr. Adams named Mr. Donlon, who has decades of experience in law enforcement and security, to steady the ship. On Monday, around 1:15 p.m., Mr. Donlon sent an internal departmentwide memo to re-steady it.
In the email to the rank and file, obtained by The New York Times, Mr. Donlon did not address the searches, which he has said were unrelated to his work with the Police Department. Instead, he began the brief message with an anecdote about his Bronx upbringing. He said he had learned about the department from his father, a civilian carpenter whose office was “every precinct” and who introduced him to officers who could serve as mentors.
“I want you to meet good people,” he recalled his father saying. Mr. Donlon learned about the department through those people, he said, “not through the newspapers, or the movies, or stories told around the neighborhood.”
He then described his work as an F.B.I. agent on the Joint Terrorism Task Force, and how collaboration among local, state and federal law enforcement agencies was now keeping the U.N. General Assembly “running smoothly.”
“It is a collective effort to work as one team, unified in our cause and secure in our purpose,” he wrote. “And it is a blueprint of how we will move this organization forward.”
The police did not immediately respond to a request for comment on Monday about the raid, which the commissioner announced in a news release late Saturday, or how it could affect Mr. Donlon’s ability to lead the department.
New York City’s police department, which has more than 50,000 civilian and uniformed employees, is unique in the scope of its work. It cooperates constantly with federal authorities on matters that involve national security and international affairs, like the General Assembly this week. The investigation of Mr. Donlon could be a hindrance as the department deals with classified matters.
On Monday morning, Tarik Sheppard, the department’s top spokesman, told NY1 that he was “supportive” of the commissioner.
“I don’t know what this is about,” he said, adding that he believed Mr. Donlon would be hiring a lawyer. “He’ll deal with the federal authorities and cooperate like he said he would.”
Asked about the reactions to the search of Mr. Donlon’s homes, a City Hall spokesman said the focus remained on keeping crime down.
“We expect all team members to fully comply with any law enforcement inquiry,” said Fabien Levy, a spokesman for Mr. Adams. “Simultaneously, we remain focused on keeping New Yorkers safe and the numbers speak for themselves, with overall crime being down for eight straight months.”
The F.B.I. declined to comment on the search of Mr. Donlon’s homes on Monday. Some city officials expressed skepticism over the timing of the search warrants.
“This can’t be serious,” Joe Borelli, a Republican and the City Council minority leader, posted on social media Saturday. “Adams hires the guy a week ago, after his own exemplary career as an F.B.I. agent, and all of a sudden the F.B.I. finds cause to search his house.”
Mr. Donlon spent his first week at the department being briefed by top executives and getting to know the command staff. On Sept. 13, when he was sworn in, he met with top chiefs and commissioners and told them he wanted leaders to act professionally and to stop fighting with reporters and critics on social media, according to two people who were briefed on the meeting.
To many inside the department, the comments were a welcome change from the vitriol and aggression that had pervaded the agency over the past several months with officials like John Chell, the chief of patrol, and Kaz Daughtry, the deputy commissioner of operations, going after reporters and local politicians on social media and sometimes in person.
But the respite was short-lived, with many wondering what could come next.
Tom Harris, a former deputy inspector, said the department was a sprawling machine with “built-in redundancy” and an organized hierarchy that could withstand the chaos that has engulfed it in recent weeks.
“Police officers are used to allegations being made against them,” he said, adding that officers and supervisors “can compartmentalize these investigations and still get the job done.”
Mr. Sheppard, in his interview with NY1, said the officers on the street “just want finality to all this.”
“Many of us want to see a conclusion to all of this, but we understand that the Southern District and the U.S. attorney have to take time to do their work,” he said.
Mr. Sheppard was then asked how he would respond to a city that might be losing confidence in the department.
“We don’t get into the mood of New Yorkers,” he said. “Our job is to keep them safe.”
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