The residents of Oakland, Calif., were already frustrated. Violent crime and burglaries had become enough of a problem that getting an In-N-Out burger and fueling up near the airport was considered a risky endeavor.

The city’s last remaining major league sports team announced in April that it would leave town after 57 seasons. And the population, currently 425,000, has been in decline since the coronavirus pandemic.

All of which served to drive signatures for a recall election against Mayor Sheng Thao only 18 months into her tenure — a rare ouster attempt in a city this large.

Then, two days after the recall qualified for the ballot last week, F.B.I. agents raided the home of Ms. Thao and stayed there for hours.

Before they scoured Ms. Thao’s house in the Oakland hills, it was possible, even likely, that she would survive the recall election this fall with the help of the same progressive allies and labor unions who supported her mayoral campaign in 2022, longtime political hands in the Bay Area said. But the raid has now cast a shadow over her future, even as she defiantly vowed on Monday to fight for her political survival.

“Everybody understands that she hasn’t been charged with a crime,” said Brenda Harbin-Forte, a retired Alameda County Superior Court judge who is a main organizer of the recall. “But our focus is that you can’t lead a city and be distracted about whether any day now you’re going to get indicted for a federal crime.”

Ms. Thao, a Democrat, has overcome immense personal struggles before. She is the daughter of working-class refugees and a survivor of domestic violence who once lived out of her car with her son when he was an infant. When she was sworn in, Ms. Thao became the most prominent Hmong American officeholder in the United States.

Few would blame her alone for the city’s woes, which were percolating well before she took over at City Hall. Crime was already on the rise, and homeless camps had proliferated since the early days of the pandemic. Two major league sports teams had already fled. The city had lost its glimmer in comparison with the previous decades in which it had attracted residents as a soulful, more affordable alternative to San Francisco.

What Oakland needed from Ms. Thao was a turnaround. The prevailing mood, however, is one of frustration.

The exact targets of the federal investigation remain unclear. The F.B.I. would not comment other than to confirm that agents had searched the home where Ms. Thao and her partner reside, as well as three other properties in Oakland that are associated with the Duong family, which runs California Waste Solutions, a local company that collects recyclables for the city. Renia Webb, Ms. Thao’s former chief of staff, said in an interview that F.B.I. agents asked her questions about Ms. Thao last year.

The raid was a political earthquake, and the fallout continued for four days as Ms. Thao disappeared from public view.

Then, on Monday, Ms. Thao came out fighting by giving brief remarks at City Hall, after which she did not take questions. She asserted that federal authorities had not given her an opportunity to cooperate with their investigation before the raid. She raised questions about the close timing of the F.B.I. search and the recall efforts.

“I want to be crystal clear: I have done nothing wrong,” she said. “I am confident that I will not be charged with a crime because I am innocent.”

David Duong, the chief executive of California Waste Solutions, said in a statement on Thursday that the company was fully cooperating with the investigation and that it was confident the government would conclude that it was not involved in any unlawful or improper activity.

Since the raid, many of Ms. Thao’s supporters who had vowed to fight on her behalf in the recall have been quiet. Those who have spoken out have hardly been enthusiastic.

Keith Brown of the Alameda Labor Council, a union that supported Ms. Thao’s campaign in 2022, said in a statement on Sunday that his members were “awaiting the facts.” Cat Brooks, a co-founder of the Anti Police-Terror Project, an organization that seeks to eradicate police violence in communities of color, lamented the “stench” that the F.B.I. raid would leave on other progressive politicians and activists in Oakland.

Ms. Thao’s critics have pounced. They were quick to point out that the Duong family has been investigated since 2019 by Oakland’s public ethics commission for allegedly bypassing campaign limits and giving money to various political candidates through “straw donors,” including to Ms. Thao during her campaign for a City Council seat. The family is politically connected and has made contributions to both Democratic and Republican politicians.

The past mayors of Oakland include Jerry Brown, who ran the city for several years between his two stints as governor. Unlike Mr. Brown, Ms. Thao became the mayor of Oakland early last year with little experience in elected office, having served one Council term.

Ms. Thao won the mayor’s race by a narrow margin through a ranked-choice vote, which allowed voters to choose candidates in order of priority and used multiple rounds of counting to determine the victor. She saw her win as an inspiration to other children of immigrants who grew up in poverty.

On Monday, she drew upon that same personal history to defend herself.

“What I do know is that this wouldn’t have gone down the way it did if I was rich, if I had gone to elite private schools or if I had come from money,” she said. “I know that for sure because former elected officials are sitting safely in their houses in the hills right now, with campaign finance violations, piling up mountains of evidence that prove actual wrongdoing.”

Less than two years into her tenure, some supporters credit Ms. Thao with finding creative solutions to close the city’s budget gaps without inflicting major cuts. She has promoted the ways her administration has added police patrols and used technology to combat crime.

Her critics concede that Ms. Thao inherited problems as Oakland was struggling to climb out of a pandemic recession. But, they say, there have been obvious missteps.

During her tenure, the city missed out on millions of dollars in state funding to combat organized retail theft because her administration failed to submit an application on time. She fired a popular Black police chief, LeRonne Armstrong, angering many residents in a city where one-fifth of the population is Black.

“Voters are already losing confidence in City Hall because of rampant homelessness, because of shooting after shooting, because we can’t even get our roads paved,” Councilwoman Janani Ramachandran, a Democrat, said.

Ms. Thao is not the only one being blamed for crime in Oakland. In April, a separate effort to recall Pamela Price, a progressive district attorney, also qualified for the ballot. Ms. Price won election in 2022 with a pledge to seek shorter sentences and to prosecute police officers who unlawfully use lethal force.

The top backers of the recall effort against Ms. Thao include Ron Conway, a billionaire tech investor and political fund-raiser who also contributed to the 2022 recall of Chesa Boudin, a Democrat who served as San Francisco’s district attorney. But recall organizers said that their campaign was more complicated than the narrative of progressive-versus-moderate, especially in Oakland, where many politicians fall along a narrow spectrum of progressive to more-progressive and the local NAACP chapter has favored a more aggressive law-and-order approach to crime.

“This is not an attack on progressives,” Ms. Harbin-Forte, the recall organizer, said. “This has to do with the people in the office who are executing those policies, and whether or not they are making the decisions that are in the best interest of everybody.”