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.

The list has generated unease inside the bureau given the mass firings at the Justice Department in recent days.

The messages showed that F.B.I. investigators took normal bureaucratic steps and precautions when opening an extraordinarily sensitive inquiry into Mr. Trump’s attempts to overturn the 2020 election.

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.

President Trump’s directive is supposed to exempt national security and public safety positions, but the F.B.I. has put an immediate hiring freeze in place.

Kash Patel, Donald J. Trump’s choice to run the bureau, has made a series of spurious assertions about the Russia, Jan. 6 and classified documents inquiries.

In exchange, the Biden administration released an Afghan man convicted on narcotics charges in 2008.

Christopher A. Wray, the former director, stepped down Sunday. Brian Driscoll, who recently took charge of the F.B.I.’s Newark field office, will be acting director, according to a White House statement.

Recordings and interviews detail Shamsud-Din Jabbar’s growing discontent with American society and increasing isolation even within his local Muslim community.