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Bongino announced his departure, which had been expected, in a post on X in which he said he was grateful for the “opportunity to serve with purpose.� He did not say precisely when in January he would leave or reveal his future plans, but President Donald Trump, in response to a question earlier in the day about Bongino's fate, said: “Dan did a great job. I think he wants to go back to his show.�

In a social media post, Patel called Bongino “the best partner I could've asked for in helping restore this FBI.� He said Bongino “had not only completed his mission — he far exceeded it. We will miss him but I'm thankful he accepted the call to serve. Our country is better and safer for it.�

Bongino was always an unconventional pick for the No. 2 job at the FBI, a position that historically has entailed oversight of the bureau’s day-to-day operations and has been typically held by a career agent. Though he had previously worked as a New York City police officer and Secret Service agent, neither he nor Patel had any experience at the FBI before being picked for their jobs. But both came in pledging overhauls to an FBI they insisted had been weaponized against Trump.

Bongino was installed in the role in March by Trump after years as a conservative podcast host, where he used his platform to repeatedly rail against FBI leadership and to promote conspiracy theories related to the Epstein sex-trafficking case and pipe bombs discovered in Washington on Jan. 6, 2021.

Once in the job, he used social media to communicate directly to Trump supporters restless over a perceived lack of action by the new FBI leadership to address their concerns. He reassured them the FBI under his watch was giving renewed attention to issues like the pipe bomb case, and the .

Yet he struggled to placate elements of Trump’s base who expected him to quickly deliver the FBI reforms he had long said were needed and to uncover the truths he claimed had been hidden by the federal government.

On the Epstein case, for instance, he had previously challenged the in a New York jail soon after his 2019 arrest. But after his arrival in the bureau, he said in a Fox News interview: “I’ve seen the whole file. He killed himself.�

Bongino had separately speculated as recently as last year that the pipe bombs placed on the eve of the Jan. 6 Capitol riot were either an “inside job" or the work of a “connected anti-Trump insider� and said the truth was shielded by a “massive cover-up.� He was confronted with those same comments when the FBI earlier this month arrested a 30-year-old Virginia man with no evident connection to the federal government, prompting skepticism from some that investigators had actually arrested the right person.

“I was paid in the past, Sean, for my opinions, that's clear,� Bongino said in a Fox News interview with Sean Hannity. “And one day, I'll be back in that space but that’s not what I’m paid for now. I’m paid to be your deputy director, and we base investigations on facts.�

Questions about Bongino's future had lingered for months, particular after a tense exchange at the White House last July with Attorney General Pam Bondi that they would not be releasing any additional records from the Epstein investigation.

After that encounter, Bongino, normally active on social media, went silent from his FBI account for several days. Far-right activist , who is close to Trump, posted on X at the time that she was told that Bongino was “seriously thinking about resigning� and had taken the day off to contemplate his future.

In August, the Trump administration took the unusual step of adding a co-deputy director, former Missouri Attorney General Andrew Bailey.

Bondi on Wednesday joined in the tributes, posting on X that Americans were safer because of Bongino's service. “Thank you, Dan," she wrote.