He dealt with the F.B.I. investigation into whether Hillary Clinton mishandled classified information when she used a private email server. Republicans, including Mr. Trump, have relentlessly criticized the F.B.I. for the way it handled that investigation. Mrs. Clinton was not charged, nor were any of her aides. Mr. McCabe has also been deeply involved in the F.B.I.’s investigation into Russia’s interference in the 2016 election and the potential involvement of the Trump campaign.

The Russia investigation is being led by a special counsel, Robert S. Mueller III, who has already charged four people associated with Mr. Trump’s presidential campaign. One of them, a foreign policy adviser, has pleaded guilty to lying about his contacts with the Russians, while another pleaded guilty to lying about his conversation with the Russian ambassador to the United States.

Mr. Mueller’s inquiry has infuriated the president, who has called the investigation a witch hunt and has pressed repeatedly for a shake-up at the F.B.I. Mr. McCabe was deputy director when the F.B.I. opened the investigation in July 2016.

The president crowed on Saturday that James A. Baker, the F.B.I. general counsel, who was seen as an ally of Mr. Comey’s, would soon step down from that post, although he will remain at the bureau.

Mr. McCabe became a political piñata after his wife decided to run as a Democrat for a Virginia State Senate seat. As part of her campaign, she accepted nearly $500,000 in contributions from the political organization of Gov. Terry McAuliffe, a longtime friend of Mrs. Clinton and her husband, former President Bill Clinton.

Pressure on Mr. McCabe and Mr. Wray intensified this month after The New York Times reported that a top F.B.I. lawyer and counterintelligence agent traded disparaging text messages about the president. Both the agency and the lawyer had worked closely on the Clinton and Russia investigations. However, Mr. Mueller decided to pull the agent off the Russia investigation. The lawyer, who was close to Mr. McCabe, had already left Mr. Mueller’s team by the time the texts were discovered.

Republicans seized on the texts to claim that the F.B.I.’s leadership was politically slanted. Agents have rejected that assertion, calling it insulting and untrue.

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Mr. McCabe, who is seen as highly intelligent, rose quickly through the ranks of the F.B.I., eventually running national security, then the bureau’s second-largest field office, before moving back to headquarters, where he was put on track to be deputy director. He has many supporters in the F.B.I. who consider him beyond reproach.

His defenders say he has done his job admirably in the face of intense partisan attacks while navigating crisis after crisis.

“The political hit job on McCabe — his supposed ideological bias, the fact his wife ran for office as a Democrat, the attacks on his competence — are way out of line,” said Frank Montoya Jr., a former senior F.B.I. official who retired in 2016 and worked closely with Mr. McCabe. “The people who are making these baseless accusations don’t know McCabe. I do. The guy’s a total pro. His only motivation is to support and defend the Constitution.”

His detractors see Mr. McCabe as an ambitious creature of Washington who did not spend enough time as an agent working with informants and making cases. Those critical of Mr. McCabe believe he lacked the operational experience to become director and needed to spend more time in the field.

But even among some of those who dislike Mr. McCabe, he earned their grudging respect when he stood up to Mr. Trump and defended the F.B.I. and Mr. Comey’s tenure during a heated congressional hearing in May while he was acting director.

Mr. McCabe’s plan to retire at some point after he was eligible to retire was first reported by The Washington Post. Mr. McCabe will most likely follow the path of other highly qualified F.B.I. senior officials eligible to retire who leave after securing a lucrative job in the private sector.

Officials say that Mr. Wray is considering David L. Bowdich, currently the third-ranking official in the bureau, to replace Mr. McCabe. Mr. Bowdich ran the F.B.I.’s Los Angeles field office before coming to Washington. He is best known for being the public face of the F.B.I. in California after the 2015 San Bernardino terrorist attack.

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