James E. Dennehy, the highly respected leader of the largest and most important field office in the bureau, said in an email to staff that the F.B.I. was in “a battle of our own.”

The prosecutor firings and a move to scrutinize thousands of F.B.I. agents were a powerful indication that the president has few qualms deploying federal law enforcement to punish perceived enemies.

Testifying in a confirmation hearing, Kash Patel, who is nominated to lead the F.B.I., also sought to allay fears about his fitness to serve.

Kash Patel exhibited unflinching fealty during Donald Trump’s four years out of office, standing by him during the grim days after the F.B.I. search of the president’s Florida estate in 2022.

The F.B.I. nominee has not only cast his political lot with the president, he has also used the connection to the Trump brand, Truth Social and other Trump-linked entities as a significant source of income over the past several years.

The move follows the resignation of the department’s chief corruption prosecutor, who chose to step down after being told the Trump administration was reassigning him to a position related to immigration enforcement.

The move was part of a domino effect initiated by President Trump’s enactment of a 90-day federal hiring freeze.

President Trump’s pardons in the Jan. 6 case abruptly ended the most complex investigation in U.S. history. It also raised questions about what he will do next against a department he has said is full of his enemies.

Donald Trump is returning to the White House vowing to seek retribution. Those in his sights are worried both about him — and his supporters.

Mr. Smith, a special counsel appointed by Attorney General Merrick B. Garland, had signaled that he would step down before Donald J. Trump’s inauguration.

The two episodes have superficial similarities, including that both suspects used the same car rental app.