The FBI agent in charge of its New York field office resigned on Monday, after he clashed with the Trump administration on multiple objectives, including its efforts to dismiss Justice Department employees who helped prosecute President Donald Trump. 

James Dennehy, who had been running the office since September, indicated that he was forced out of the bureau on Friday, as the FBI looks to shake up its senior ranks. 

Dennehy allegedly upset the new administration by supporting DOJ officials who did not want to turn in employees who helped prosecute Trump and January 6 rioters. He also reportedly upset Attorney General Pam Bondi over his office's handling of the Jeffrey Epstein files last week, according to the New York Times.

“Late Friday, I was informed that I needed to put my retirement papers in today, which I just did,” Dennehy wrote in an email to colleagues. “I was not given a reason for this decision. Regardless, I apologize to all of you for not being able to fulfill my commitment to you.”

The announcement comes after Bondi told new FBI Director Kash Patel that she had been "repeatedly assured" that she was given all documents related to Epstein, but had in fact only received small fraction of that paperwork.

“When you and I spoke yesterday, you were just as surprised as I was to learn this new information,” she wrote, before imposing a new Feb. 28 deadline to “deliver the full and complete Epstein files to my office.” 

Bondi also ordered the FBI to investigate agents who had failed to produce the documents. 

Dennehy's exit marks the end of his 23-year career in the bureau. He joined in 2002, after he served seven years as a U.S. Marine officer. Throughout his storied career, he primarily investigated or supervised counterintelligence cases.

Misty Severi is a news reporter for Just The News. You can follow her on X for more coverage.