Rebecca Weiner learned about catastrophic threats at an early age: She grew up in Santa Fe, N.M., near the cradle of the nuclear bomb.

Her grandfather, a mathematician, fled Poland in 1939, studied at Harvard and then moved to New Mexico in 1943 to help develop atomic weapons. In college, Ms. Weiner studied the ethical questions that Manhattan Project scientists, and their wives, confronted as they devised the bombs that annihilated two Japanese cities, but that they hoped would “end war as we know it,” she said.

Now, Ms. Weiner, 46, has been named the New York Police Department’s deputy commissioner of intelligence and counterterrorism, commanding about 1,500 people spread throughout the city. The bureau includes dozens of analysts and hundreds of officers and investigators who monitor threats like bomb plots, mass shootings and spontaneous chaos like a social media influencer’s video game giveaway that drew thousands of rowdy teenagers to Union Square this month.

A lawyer and 17-year department veteran, Ms. Weiner is taking over a bureau that includes a counterterrorism unit created after the Sept. 11 attacks. Since its inception, the unit has helped foil a plan to kidnap an American-Iranian journalist and what officials say were dozens of terrorist plots.

It is also a bureau whose work remains shrouded in secrecy and that has been condemned because of its surveillance activities, including in 2011, when the public learned that its officers had been spying on Muslims for years.

The bureau has been most visible when it has violated civil liberties, but Ms. Weiner said in an interview that it had protected them more conscientiously in the past decade. The unit’s focus, now, she said, was on stopping so-called lone wolves like the man who massacred Black residents of Buffalo at a supermarket, the truck driver who mowed down eight people on a Manhattan bike path and the man who stabbed the author Salman Rushdie last August in Chautauqua, N.Y.

In the interview, Ms. Weiner ticked off some of the threats New York City currently faces: the Islamic State, right-wing extremists and accelerationists, a white supremacist movement that advocates overthrowing the government.

“The individual actor has been the biggest concern for a while,” she said, adding that what kept her awake was “the concern that we’ve missed something.”

Ms. Weiner, who was sworn in last month as her two sons, 5 and 8, held a Bible, is the rare top police executive who does not have close personal ties to Mayor Eric Adams, a former police captain who identifies closely with the force. Rather than walking a neighborhood beat, she joined as a civilian junior analyst with a law degree.

In 2020, during a panel discussion hosted by the Global Security Forum, an annual gathering of experts and officials, the moderator — a woman — asked Ms. Weiner whether she led with “tough love mothering” or by embracing a “flirtatious, more traditional vamp style.”

Ms. Weiner was silent for a moment.

“I hope those aren’t the only two options,” she replied, then burst out laughing.

“I am going to be who I am,” Ms. Weiner told the moderator. “And that’s how I’m going to lead from wherever I am in the organization.”

Reassuring residents of the bureau’s intentions and practices is a crucial task for Ms. Weiner as police departments in general confront “an erosion of trust,” said William J. Bratton, who met her when he returned to lead the department for a second term as commissioner in 2014.

Ms. Weiner’s intellect, humor and approachability should help, Mr. Bratton said.

“One of the reasons she collaborates so well with people is that she makes her points without alienating people,” he said.

Ms. Weiner said that the participation of her grandfather, Stanislaw Ulam, in the most secret military initiative of World War II influenced her career choices.

“I was always interested in national security work, in protecting our country,” she said.

Mr. Ulam, Ms. Weiner said, played memory games with her when she was a child to test how the brain resembled a computer. But she was particularly fascinated by her grandmother, Francoise Aron Ulam, who came to the United States from France and met Mr. Ulam in 1941.

Ms. Ulam spoke three languages, helped write her husband’s memoirs and worked as a “calculator” on the Manhattan Project along with other wives, performing complex mathematics using paper, pencil and slide rules.

Ms. Weiner grew up wanting to learn more about her and the other young women who relocated to Los Alamos so their husbands could work on “the Gadget,” the nickname for the bomb.

“Many of them were really grappling with the same ethical quandaries as their husbands, but without the exhilaration of knowing that they were in charge of the scientific discovery,” Ms. Weiner said.

She helped her grandmother write her own memoirs as a student at Harvard, where she majored in history and literature and met her husband, Drake Bennett, a reporter at Bloomberg News. She earned a law degree at Harvard, then began researching international security as a fellow at the John F. Kennedy School of Government’s Belfer Center for Science and International Affairs.

When she joined the Police Department in 2006, she was one of only a few female analysts. She rose through the ranks, becoming director of intelligence analysis in 2012 and assistant commissioner of the intelligence bureau in 2016.

John Miller, who became deputy commissioner of the bureau in 2014, said she had a “remarkable” ability to recognize how security threats were changing.

“Whether it was the shift to Al Qaeda to ISIS, or the shift from sleeper cells to lone wolves to domestic-inspired racism, it was Rebecca and her team of analysts who were always on the cutting edge,” Mr. Miller said.

By the time Ms. Weiner joined the department, the counterterrorism division had developed a secret demographics unit composed of officers whose job was to create a map that showed where different ethnic groups lived. The goal was to learn where terrorist suspects could blend in, but the unit’s tactics shifted into a blanket surveillance of Muslims and developing databases of where they shopped, worked and prayed.

The unit was exposed in 2011 by The Associated Press, prompting lawsuits by Muslim and civil liberties groups, who said the tactics violated the rules that had been established as a result of a 1970s case involving the department’s spying on students, civil rights groups and suspected Communist sympathizers. Known as the Handschu case, the litigation led to federal guidelines prohibiting the Police Department from collecting information about political speech unless it is related to potential terrorism.

Ms. Weiner did not work in the demographics unit, but she helped handle negotiations between the department and lawyers for the plaintiffs in the suits filed after the unit’s tactics were exposed.

“There was a level of mistrust that we had to rectify,” she said.

Jethro Eisenstein, a lawyer for plaintiffs in the Handschu case, said Ms. Weiner had shown a strong regard for civil liberties. During one negotiation session in 2016, Ms. Weiner asked hypothetically whether the bureau should investigate someone who had declared support for ISIS online.

Of course it should, the lawyers replied. Her response was surprising, Mr. Eisenstein recalled.

“‘Really? Just based on that?’” she said.

“She was reviewing a lot of things that people said and then trying to decide whether that warranted a disruption of their lives,” Mr. Eisenstein said. “She was really putting on the brakes.”

Ms. Weiner and other police officials now meet monthly with a civilian representative who reviews the department’s investigations and reports potential wrongdoing to a federal judge. The representative has submitted five reports since 2018. All found the department in compliance with the guidelines.

Naz Ahmad, the acting director of the CLEAR project, one of the organizations that sued the department over the spying program, said the representative had helped police officials consider how their work affects civil liberties. Still, Ms. Ahmad added, the department did not have to detail its online investigations or divulge the race or religion of its targets.

In 2016, the city’s inspector general found that in more than 95 percent of case files, the targets of investigations “were predominantly associated with Muslims” or engaged in political activity associated with Islam.

“We have no insight into whether those numbers have changed,” Ms. Ahmad said.

Ms. Weiner said the bureau did not track the race and ethnicity of people it was investigating, but she said the demographics would be different today, given how the threats had shifted to right-wing extremism.

Often, she said, the threats came from people driven by conflicting ideologies, like Ethan Melzer, a soldier who consumed both ISIS and neo-Nazi propaganda before hatching a plan to kill U.S. service members.

Ibrahim Bechrouri, who teaches surveillance and counterterrorism at the John Jay College of Criminal Justice, said the bureau Ms. Weiner now oversees remains too secretive.

“It still does not have enough oversight,” he said. “We don’t have any transparency on what is happening now when it comes to the use of new technologies.”

Ms. Weiner said the bureau shares information “whenever we can.”

“Ultimately, our job is to protect people,” she said. “We’re not withholding information to benefit us. We want to protect people’s lives.”