Officials said Mr. Wray cannot be seen inside the F.B.I. as dismantling the existing management team merely because the president does not approve of it — a move that would appear political and hurt the director's standing among agents.
Many of Mr. Wray's senior leadership team members were promoted under Mr. Comey, including Andrew G. McCabe, the embattled deputy director. Mr. Wray has to decide on the future of Mr. McCabe, who has been singled out by Mr. Trump because of his wife's political activities and because of his role as deputy director during the Clinton email investigation.
In 2015, Mr. McCabe's wife, Jill McCabe, ran as a Democrat for a Virginia State Senate seat and 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.
Officials said that Mr. McCabe is seen inside the F.B.I. as a distraction for Mr. Wray — and a punching bag for Mr. Trump and Republicans who have tried to turn him into a prominent example of political bias at the bureau. In private conversations, Mr. Trump has groused that Mr. Wray has not swiftly removed people whom he perceives as loyal to Mr. Comey.
Even agents who believe that Mr. McCabe is being treated unfairly agree that, for Mr. Wray to succeed, he will most likely have to choose a new deputy.
Officials say that Mr. Wray is leaning toward promoting David L. Bowdich, currently the third ranking official in the bureau. He is well liked inside the F.B.I. and is seen as someone who was not part of Mr. McCabe's inner circle. Mr. Bowdich, the former top agent in the Los Angeles Field Office, is best known for being the public face of the F.B.I. in California after the 2015 San Bernardino terrorist attack.
Other changes are already in the works. On a conference call on Wednesday, it was announced that James A. Baker, the F.B.I. general counsel who was seen as an ally of Mr. Comey's, would step down from that post, although he will remain at the bureau. Mr. Baker provided counsel to Mr. Comey during the investigation into Mrs. Clinton's emails.
Mr. Wray has so far avoided a public dispute with Mr. Trump, primarily leaving the job of defending the bureau to former F.B.I. officials. In the December hearing before the House Judiciary Committee, he did push back against some of the president's comments, albeit in a nonconfrontational way.
If Mr. Trump continues to go after the F.B.I., however, Mr. Wray might have to change course and risk a blowup. F.B.I. agents want to know that the director has their back.
"The troops need to know and understand that he has their best interests in heart," Mr. Yacone said. "I think he is doing this to the best of his abilities under the extraordinary circumstances."
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