A 39-year-old woman took Flight 701 from Doha, Qatar, to John F. Kennedy International Airport in late February, the final leg of her trip home to New York City from Iran.

A week later, on March 1, she tested positive for the coronavirus, the first confirmed case in New York City of an outbreak that had already devastated China and parts of Europe. The next day, Gov. Andrew M. Cuomo, appearing with Mayor Bill de Blasio at a news conference, promised that health investigators would track down every person on the woman’s flight. But no one did.

A day later, a lawyer from New Rochelle, a New York City suburb, tested positive for the virus — an alarming sign because he had not traveled to any affected country, suggesting community spread was already taking place.

Although city investigators had traced the lawyer’s whereabouts and connections to the most crowded corridors of Manhattan, the state’s efforts focused on the suburb, not the city, and de Blasio urged the public not to worry. “We’ll tell you the second we think you should change your behavior,” the mayor said March 5.

For many days after the first positive test, as the coronavirus silently spread throughout the New York region, Cuomo, de Blasio and their top aides projected an unswerving confidence that the outbreak would be readily contained.

There would be cases, they repeatedly said, but New York’s hospitals were some of the best in the world. Plans were in place. Responses had been rehearsed during “tabletop” exercises. After all, the city had been here before — Ebola, Zika, the H1N1 virus, even Sept. 11.

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“Excuse our arrogance as New Yorkers — I speak for the mayor also on this one — we think we have the best health care system on the planet right here in New York,” Cuomo said on March 2. “So, when you’re saying, what happened in other countries versus what happened here, we don’t even think it’s going to be as bad as it was in other countries.”

But now, New York City and the surrounding suburbs have become the epicenter of the pandemic in the United States, with far more cases than many countries have. More than 138,000 people in the state have tested positive for the virus, with nearly all of them in the city and nearby suburbs.

On Tuesday, Cuomo announced that 731 more people had died of the virus, the state’s highest one-day total yet. The overall death toll in New York is 5,489 people.

Epidemiologists have pointed to New York City’s density and its role as an international hub of commerce and tourism to explain why the coronavirus has spread so rapidly. And it seems highly unlikely that any response by the state or city could have fully stopped it.

From the earliest days of the crisis, state and city officials were also hampered by a chaotic and often dysfunctional federal response, including significant problems with the expansion of coronavirus testing, which made it far harder to gauge the scope of the outbreak.

Normally, New York would get help from Washington in such a time, as it did after Sept. 11. But President Donald Trump in February and early March minimized the coronavirus threat, clashing with his own medical experts and failing to marshal the might of the federal government soon after cases emerged in the United States.

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As a result, state and city officials often had to make decisions early on without full assistance from the federal government.

Even so, the initial efforts by New York officials to stem the outbreak were hampered by their own confused guidance, unheeded warnings, delayed decisions and political infighting, The New York Times found.

“Flu was coming down, and then you saw this new ominous spike. And it was COVID. And it was spreading widely in New York City before anyone knew it,” said Dr. Thomas R. Frieden, the former head of the Centers for Disease Control and Prevention and former commissioner of the city’s Health Department. “You have to move really fast. Hours and days. Not weeks. Once it gets a head of steam, there is no way to stop it.”

Frieden said that if the state and city had adopted widespread social-distancing measures a week or two earlier, including closing schools, stores and restaurants, then the estimated death toll from the outbreak might have been reduced by 50% to 80%.

But New York mandated those measures after localities in states including California and Washington had done so.

San Francisco, for example, closed schools on March 12 when that city had 18 confirmed cases; Ohio also closed its schools the same day, with five confirmed cases. De Blasio ordered schools in New York to close three days later when the city had 329 cases.

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Then seven Bay Area counties imposed stay-at-home rules on March 17. Two days later, the entire state of California ordered the same. New York state’s stay-at-home order came on the 20th, and went into effect on March 22.

“New York City as a whole was late in social measures,” said Isaac B. Weisfuse, a former New York City deputy health commissioner. “Any after-action review of the pandemic in New York City will focus on that issue. It has become the major issue in the transmission of the virus.”

Interviews with more than 60 people on the front-lines of the unfolding crisis — city and state officials, hospital executives, health care workers, union leaders and emergency medical workers — revealed how the virus overwhelmed the city’s long-standing preparations, leaving officials to improvise. Many spoke on the record; others spoke anonymously to describe private meetings and conversations without fear of losing their jobs.

“Everything was slow,” said Councilman Stephen T. Levin, D-Brooklyn, who had called for City Hall to take swifter action as the outbreak spread. “You have to adapt really quickly, and nothing we were doing was adapting quickly.”

Both Cuomo and de Blasio have focused intensely in recent days on vastly expanding the ability of the health care system to treat coronavirus patients as the outbreak nears its peak. The state and city have set up new hospital wards, scoured the world for ventilators and protective gear, and aggressively recruited doctors and nurses around the country.

Cuomo has been praised for his informative daily news conferences, where he not only focuses on the facts of the pandemic but also seeks to rally the public’s support for efforts to curb the spread. De Blasio has also made outreach a priority.

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Still, Cuomo has at times acknowledged the difficulties in fighting the outbreak. “I am tired of being behind this virus,” he said March 31. “We’ve been playing catch-up. You don’t win playing catch-up.”

The governor’s aides said he was referring to the country as a whole, not New York.

The governor and the mayor emphasized that they had no misgivings about their initial handling of their response. They said that their efforts spurred the Trump administration to act more decisively to curb the outbreak. New York was the first state to obtain federal approval for its own coronavirus testing.

“Every action I took was criticized at the time as premature,” Cuomo said in an interview. “The facts have proven my decisions correct.”

De Blasio said in a statement, “We’re dealing with a virus that’s only months old and science that changes by the day,” adding that “hindsight is a luxury none of us have in the heat of battle.”

Confidence and confusion

From the start, de Blasio and Cuomo projected as much concern about panic as they did about the virus.

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“We can really keep this thing contained,” de Blasio said at a news conference about virus preparations in late February.

That tone continued even after the first positive case was announced March 1.

“Everybody is doing exactly what we need to do,” said Cuomo, seated with de Blasio, at a news conference on March 2. “We have been ahead of this from day one.”

Hospitals also expressed confidence in their plans for responding to a pandemic, with the Healthcare Association of New York State declaring on March 2 that its members were “prepared for an influx of patients caused by COVID-19.”

But few, if any, appeared to have made significant efforts before the virus hit to greatly increase supplies of ventilators or protective gear, looking instead to draw on emergency government stockpiles.

Officials seemed to speak and act based on the assumption that the virus had not arrived in the state until that first case — the woman traveling from Iran. State and local officials now acknowledge that the virus was almost certainly in New York much earlier.

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Infectious disease specialists had known for weeks before any positive test had occurred that many of the early cases would be missed because of significant flaws in federal testing.

Bruce Farber, the chief of infectious diseases for two hospitals within Northwell Health, the largest hospital system in New York, said that by late January, it was apparent that cases would soon begin appearing in the United States. He said he and his colleagues realized, as they reviewed the strictly limited federal testing criteria during a Feb. 7 meeting, that many infected people would not be identified.

Only those with a fever severe enough to require hospitalization and who had traveled to China in the previous 14 days could get tested, Farber told them, reading from the CDC guidelines.

“It was that moment that I think everybody in the room realized, we’re dead,” Farber said.

For both city and state, the initial plan was to trace, isolate and contain each case. Cuomo promised that they would go further than necessary to find every connection to the woman who arrived from Iran.

“Out of an abundance of caution we will be contacting the people who were on the flight with her from Iran to New York,” he said.

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But no one ever did that work. Local officials could only request an investigation from the CDC, and the agency did not perform one because they believed at the time she had not been contagious during the flight, officials said. Neither Cuomo nor de Blasio publicly mentioned finding the plane passengers again.

That’s because new cases in the area kept emerging: the lawyer in New Rochelle who worked in Manhattan but had no connection to the first case and had not traveled to countries affected by the virus. Then two more people in New York City tested positive, also unconnected to the affected countries and, more ominously, to each other.

New York City, at the start of the outbreak, relied on 50 disease detectives to trace the rapidly rising cases of unconnected infected people, city officials said.

By comparison, in Wuhan, China, where the pandemic began, more than 9,000 such workers were deployed. New York City added to its original 50 only after the outbreak began to accelerate.

Because of the limits on testing, said the mayor’s press secretary, Freddi Goldstein, “all the detectives in the world would have been useless.”

By March 5, de Blasio seemed to acknowledge the virus had spread beyond control. “You have to assume it could be anywhere in the city,” he said.

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Still, not wanting to cause undue alarm, he told New Yorkers to go on with their normal lives, which left many confused about the danger they faced.

The city’s health commissioner, Dr. Oxiris Barbot, had sought to reassure commuters, in early February, that “this is not something that you’re going to contract in the subway or on the bus.” The mayor reiterated the point several times in early March.

But there seemed to be little basis for that confidence.

The CDC in early February said it was “unclear” if the virus could be transferred on surfaces and, by March, said that it might “be possible” for someone to get infected by touching a contaminated surface and then touching their face. The virus mainly spreads between people in close contact, the agency has said, such as occurs on a crowded subway.

State and city officials blamed the confusing messages on shifting guidance from the federal government.

But by the second week in March, as the virus continued to spread widely, de Blasio also clashed over messaging with his own Health Department.

The mayor wanted widespread testing, but senior Health Department officials believed it was a waste of limited resources. They urged instead a public awareness campaign to tell people with mild symptoms to stay home and not infect others, or themselves, by going to testing centers.

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City Hall blocked the department from releasing that message to the public, until the mayor eventually backed down in the third week in March.

Alarm behind the scenes

New York City’s system for detecting infectious diseases was flashing danger.

While only about 100 cases of the coronavirus had been confirmed in the whole state, the city’s surveillance system was, by the end of the first week in March, signaling a spike in influenza-like illnesses at emergency rooms. A few days later, the number of police officers calling out sick jumped noticeably, as did calls to 911 for fever and cough.

The governor and the mayor began taking limited steps to restrict people’s activities, but even those were met with resistance.

Locals complained when the governor ordered a porous “containment area” for New Rochelle, where a cluster had emerged. It meant closing schools and gathering places in a 1-mile radius of a synagogue at the center of the outbreak, while allowing movement in and out.

But the biggest and most prolonged battle centered on closing the city’s school system, with its 1.1 million students. Doing so would amount to a virtual shutdown of the city.

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The mayor and his aides worried about the effect on the poorest and most vulnerable New Yorkers. For de Blasio, whose progressive political identity has been defined by his attention to the city’s have-nots, the crisis presented a stark and unwelcome choice to harm some New Yorkers in order to save others.

“If you suddenly in one day close down the schools, how do you make sure that you are providing for these kids and their parents?” said Emma Wolfe, a top aide to de Blasio. “We’re not in the suburbs. We can’t tell people to stay at home and play around in your yard.”

Behind the scenes, top health officials were growing increasingly alarmed. Demetre Daskalakis, the city’s head of disease control, threatened to quit if the schools were not closed, a city official said.

And Barbot — who at the start of the outbreak had insisted that “New Yorkers remain at low risk” — gave a far scarier assessment to a closed-door meeting of business executives in City Hall on March 12: Up to 70% of city residents could become infected.

The time for containment was over, she added. De Blasio, seated beside her at the meeting, stared daggers as she spoke.

“Why don’t you shut down restaurants now?” a chief executive who attended the meeting recalled someone asking the mayor.

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“I’m really concerned about restaurateurs; I’m really concerned about jobs,” the mayor responded, the executive recalled. De Blasio had urged New Yorkers to start social distancing and work from home where possible.

The following weekend, even though de Blasio and Cuomo had ordered occupancy limits for restaurants and bars, much of the city’s nightlife appeared to continue apace.

Governor vs. mayor, again

State and city officials believed they were doing everything possible to confront the outbreak, moving from big decision to big decision so quickly that each day, they said, felt like a year. They blamed the spread in New York on the federal government, which they say dragged its feet on testing. For weeks, Trump brushed aside concerns that the outbreak would damage the country.

“We have it totally under control,” Trump said in late January. A month later, he advised Americans to “view this the same as the flu.”

But local officials did have control over closing schools and businesses. While they waited on making a decision, other major cities were moving toward shutdowns.

In California, Los Angeles followed San Francisco’s lead and closed its schools on March 13, after 40 cases of the virus had been confirmed. On that same day, there were nearly four times as many confirmed cases in New York, but the city’s schools remained open.

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Even as aides to the mayor and governor, both Democrats, worked closely together on the response, old rivalries crept in. Though the two leaders put up a unified front at the outset of the outbreak, it was clear by the middle of March that a high-stakes version of their long-standing political battles was playing out. The March 2 news conference has been their only appearance together.

First, Cuomo sought to force the mayor’s hand on the schools, state officials said.

In a series of calls during the second weekend in March, the governor worked with the Greater New York Hospital Association, a powerful hospital lobby, to address the question of child care for health care workers in the event that schools closed. That had been a sticking point for those workers’ union, 1199 SEIU, which has deep ties to City Hall. The hospital association volunteered to raise funds.

The union, which had questioned the need to close schools on that Friday, was by Sunday calling for closure.

That Sunday morning, March 15, Health Department officials gave de Blasio some chilling forecasts of the number of possible dead if more restrictions were not imposed. Closing schools was necessary, and most businesses too. By then, the city had a plan to create centers for the children of health care workers, as well as emergency medical workers.

Finally, de Blasio was persuaded.

More on the coronavirus outbreak

As the city prepared an announcement to close the schools, Cuomo announced the shutdown during a television appearance. De Blasio made it official that evening, and then announced restaurants and bars would be closed for everything but takeout and delivery.

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After the decision on schools, the mayor became more assertive in suggesting major changes in daily life.

New Yorkers would probably soon have to be kept at home for all but the most necessary needs, he said on March 17 — a “shelter-in-place” order similar to what had already been implemented in the Bay Area of California.

This time, Cuomo was the one who resisted. He favored a more gradual shutdown.

“I’m as afraid of the fear and the panic as I am of the virus, and I think that the fear is more contagious than the virus right now,” the governor said when asked two days later about the mayor’s comments.

He chastised the mayor for a poor communication strategy.

But then California moved first: Gov. Gavin Newsom issued a statewide order for residents to stay at home. The state had 675 confirmed cases of the virus.

That same day, March 19, New York had more than 4,152.

That night, roughly 20 prominent New York leaders — including local members of Congress, two borough presidents, City Council members and civic and religious figures — joined a conference call convened by the state attorney general, Letitia James.

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“I was growing very frustrated over the schism between the mayor and the governor,” said one person on the call, who captured the sentiment. After the call, a participant conveyed those feelings to the governor’s office.

Melissa DeRosa, the governor’s top aide, said Cuomo decided on his plan to “pause” New York during an afternoon meeting with his health commissioner, before the call or Newsom’s order.

The governor had been reviewing disturbing projections about the spread of the virus since 4:30 a.m., she said.

“OK, let’s shut it down,” she recalled the governor saying. He announced it the next day.

By that point, March 20, the state had more than 7,000 confirmed cases.

The city reels

Leaders of the New York Police Department now start each day with a review of how many of its 36,000 uniformed officers are sick. By early April, it was around 19%.

“It’s been a struggle,” said the police commissioner, Dermot F. Shea. Only the fact of a shutdown city has helped.

No parades or protests. No calls to schools. Fewer calls for police in general. The calls to 911, instead, are mostly for ambulances. First it was 5,000 a day. Then 6,000. A record almost daily.

That New York City, mammoth and interconnected, would be hit hard by the pandemic may have been inevitable. But Washington, and then New York, had options. The state’s leaders had power over key decisions.

Their aides argue they moved as fast as possible given the flawed information they had from the federal government and in the midst of a fast-moving crisis on a scale none had seen before.

“This is an enemy that we have underestimated from day one,” Cuomo said Monday. “And we have paid the price dearly.”

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