WASHINGTON — President Trump’s words about Marie L. Yovanovitch, his former ambassador to Ukraine, were ominous. In a telephone conversation that has set off a political crisis for Mr. Trump, he told Volodymyr Zelensky, the president of Ukraine, that she was “bad news.”
“She’s going to go through some things,” he added.
In fact, she already has gone through quite a bit. Over the past several months, Ms. Yovanovitch, a decorated 33-year veteran of the State Department, had been vilified in the right-wing news media, denounced by the president’s eldest son as a “joker,” called a Democratic stooge by the president’s personal lawyer and then abruptly recalled from Kiev this May, months ahead of schedule.
Her supposed sin, never backed up by actual evidence, was that she had shown disloyalty to Mr. Trump, disparaging him behind his back. Her friends, who say her professionalism and history of diplomatic service make that highly unlikely, have another theory: She had turned into collateral damage in efforts by Mr. Trump and Rudolph W. Giuliani, his personal lawyer, to damage the reputation of former Vice President Joseph R. Biden Jr., perhaps Mr. Trump’s most prominent Democratic rival in 2020.
Among the apparent strikes against her: A former Ukrainian prosecutor claimed in an interview with The New York Times that Ms. Yovanovitch had blocked his team from getting visas to the United States to deliver damaging information about Mr. Biden and his son Hunter to the F.B.I.
In targeting Ms. Yovanovitch, former colleagues say, Mr. Trump and his allies underscored how profoundly suspicious they are of the career government professionals around them, leading the president to bypass the usual procedures and staff while outsourcing aspects of foreign policy to Mr. Giuliani and others.
Although largely unknown to the outside world, Ms. Yovanovitch has now become a sort of heroine to the State Department’s career staff — as well as a cautionary tale to many longtime American diplomats and national security officials. To them, she symbolizes an atmosphere in which dissenting, or even insisting on established procedures, can get them marked as outsiders, shut out of meetings, excluded from policymaking and in the end publicly hung out to dry as enemies of the administration.
At a news briefing on Thursday in New York, Secretary of State Mike Pompeo refused to answer questions shouted by reporters about why Ms. Yovanovitch had been suddenly recalled to Washington.
The American Academy of Diplomacy reacted by demanding that the State Department protect Ms. Yovanovitch from reprisals, calling the “threatening tone” of Mr. Trump’s remarks about her “very troubling.” The American Foreign Service Association, which represents State Department employees, urged that the American diplomatic corps “not be dragged into partisan political battles.”
Now serving as a diplomat in residence at Georgetown University, Ms. Yovanovitch did not respond to requests for an interview.
While the abrupt end to her ambassadorship was widely seen as punitive, one former colleague said that it was possibly motivated by a genuine concern for her, and that State Department officials decided it was safer to bring her home.
Nonetheless, the level of suspicion and paranoia inside the foreign policy and national security agencies, already high since Mr. Trump’s arrival, has only risen since Ms. Yovanovitch’s saga has surfaced.
“It’s more than crazy — it’s ugly, it’s threatening,” said Daniel Fried, a former ambassador and 40-year State Department official who has long dealt with Russian and Ukrainian issues and retired at the beginning of the Trump administration. “Masha Yovanovitch is known as a straight arrow, disciplined, professional.”
“If you take out Masha Yovanovitch, you send the message to every ambassador that we will not have your back,” he said.
Ms. Yovanovitch was born in Canada, moved to Connecticut at age 3 and became a naturalized American citizen at 18. In congressional testimony, she said her father fled the Soviet Union and then the Nazis; her mother grew up “stateless” in Germany. She said that background gave her a special empathy for those who had endured poverty, war and displacement.
She grew up speaking Russian, graduated from Princeton and joined the State Department six years later. Her specialty was Eurasia.
President George W. Bush appointed her ambassador to Kyrgyzstan, then to Armenia. President Barack Obama named her ambassador to Ukraine in 2016. There, she spoke out strongly against corruption in the Ukrainian government and pushed for a variety of reforms, including ending the immunity enjoyed by legislators accused of crimes.
John E. Herbst, a former ambassador to Ukraine, described her as a highly skilled and meticulous diplomat who would never share her personal political opinions with foreign officials — or even with her diplomatic colleagues. She was careful not to overstep her authority, he said.
“Masha is someone who is always very attentive to propriety and to instructions, and by nature, cautious,” he said. “She is uniformly held in high regard.”
The campaign against her by Trump allies began more than a year ago, with a letter from Pete Sessions, a Texas Republican member of the House at the time who lost his re-election bid in November. He wrote to Mr. Pompeo that Ms. Yovanovitch should be fired for privately and repeatedly expressing “disdain” for the current administration.
Then, this spring, Joseph E. diGenova, a former federal prosecutor and informal legal adviser to Mr. Trump, alleged on a Fox News broadcast that the ambassador had disparaged Mr. Trump to Ukrainian officials, telling them “not to listen to him or obey his policy because he was going to be impeached.”
Two days later, Donald Trump Jr. posted a link on social media to a conservative website that described her as an anti-Trump Obama loyalist, and one Mr. Trump had been trying to fire for a year. He said his father’s administration should have “less of these jokers as ambassadors.”
About the same time, a Ukrainian-American named Lev Parnas, who has worked with Mr. Giuliani, told people in Republican circles in Washington of tape recordings of conversations in which Ms. Yovanovitch had supposedly disparaged the president, according to people he spoke with. The existence of those recordings has not been substantiated.
Her troubles mounted as Mr. Giuliani stepped up pressure on the Ukrainian government to open an investigation into whether Mr. Biden, as vice-president, had forced out a top prosecutor in order to shut down an inquiry that might have implicated Mr. Biden’s son Hunter.
No evidence has emerged that Mr. Biden was actually trying to protect his son; in fact, many Western leaders viewed Ukraine’s top prosecutor as corrupt and were pressuring Ukraine’s leader to fire him.
But one former Ukrainian prosecutor, Kostiantyn H. Kulyk, told The New York Times in an interview in April that Ms. Yovanovitch had thwarted his efforts to meet with the F.B.I. to deliver damaging information about the Bidens by denying him a visa.
Mr. Giuliani also accused her of being a pawn of the New York financier George Soros, a major Democratic donor who backed a nonprofit anti-corruption group that worked in Ukraine. “The ambassador there is in the pocket of Soros,” he said in a March interview with The New York Times.
The critiques of Ms. Yovanovitch clearly reached Mr. Trump’s ears. In the July 25 phone call, Mr. Zelensky, Ukraine’s newly elected president, told Mr. Trump: “You were the first one who told me that she was a bad ambassador,” adding that “I agree with you 100 percent.”
The premature end to Ms. Yovanovitch’s tenure in Kiev was all the more remarkable because Ukraine’s government had just turned over with the surprise election of Mr. Zelensky in April.
“She’s capable and she’s tough, and why would you want to lose your ambassador right at the moment when there is a big change in the government?” asked Evelyn Farkas, a former deputy assistant defense secretary for the region that includes Ukraine.
Mr. Trump has not yet chosen a replacement.