By the time FBI Director Kash Patel took office in February, the investigation into whether John Bolton mishandled classified information had been in the works for roughly three years.
President Donald Trump had long been calling for Bolton – and other perceived political enemies – to be prosecuted, and the Maryland US Attorney’s office had been quietly building a case that started during the Biden administration.
When Patel was briefed on Bolton and other sensitive investigations shortly after landing at the bureau, he was surprised at the amount of evidence gathered.
“Why isn’t this m*therf**ker in jail yet?” Patel said after being briefed, sources familiar with the exchange told CNN.
Bolton, who served as Trump’s national security adviser in 2018 and 2019, is now the third Trump critic to be indicted in the past month after the president implored Attorney General Pam Bondi in a social media post he thought was a private message: “We can’t delay any longer, it’s killing our reputation and credibility.”
Within days of that message urging Bondi to act, Comey was indicted on charges of lying to Congress. Soon after, New York Attorney General Letitia James was charged with bank fraud related to a mortgage in an indictment unveiled last week. But while Trump called in his post specifically for the prosecutions of Comey, James and California Democratic Sen. Adam Schiff, he never mentioned Bolton in his missive.
The cases against Comey and James were presented to a grand jury by Lindsey Halligan, an interim US attorney handpicked by Trump for the position after the previous US Attorney for the Eastern District of Virginia was forced out amid pressure to bring the cases.
Halligan, Trump’s former personal lawyer who had no previous prosecutorial experience, was the only prosecutor to sign both indictments.
In contrast, six prosecutors, including US Attorney for Maryland Kelly Hayes and the current head of counterintelligence investigations at the Justice Department, Scott Lara, signed the 26-page indictment against Bolton.
In it, prosecutors accused Bolton of sharing “more than a thousand pages of information about his day-to-day activities” through his personal email account with two unauthorized individuals, who CNN has reported are his wife and daughter.
Unlike prosecutions brought against Comey and James, the Bolton case has maintained the support of career prosecutors and investigators, people briefed on the matter said. That hasn’t stopped Trump from repeatedly attacking Bolton and possibly causing damage to the case, some Justice officials fear.
Trump has railed for years against Bolton over his 2020 memoir that was highly critical of the president, claiming he should have gone to jail because classified information was contained in the book. Trump’s first Justice Department opened criminal and civil investigations into the book in 2020.
“I think he’s, you know, a bad person. I think he’s a bad guy,” Trump said Thursday when told Bolton had been indicted, adding that he had not reviewed the case.
Bolton made his initial court appearance in Greenbelt, Maryland, on Friday morning, pleading not guilty to all 18 counts. He said in a statement Thursday that he was a victim of Trump’s weaponization of the Justice Department.
“These charges are not just about his focus on me or my diaries, but his intensive effort to intimidate his opponents, to ensure that he alone determines what is said about his conduct,” Bolton said. “I look forward to the fight to defend my lawful conduct and to expose his abuse of power.”
In June 2021, the Justice Department closed its year-old criminal investigation that scrutinized whether Bolton’s 2020 book had illegally revealed national security information.
Around the same time, an Iranian hack of Bolton’s AOL email account would set in motion a new probe that led to Thursday’s charges.
On July 6, 2021, a Bolton representative notified the FBI that he was the victim of an email breach by suspected Iranian hackers.
Investigators have been laboring on this case since then after the FBI began assessing potential damage from the hack and raised questions about whether Bolton’s practice of sending diary entries from his personal email broke the law, according to people briefed on the probe.
The Iranian hacking campaign targeting Bolton and other former government officials included threats against Bolton to expose him and cause him problems of the kind that crippled Hillary Clinton’s 2016 presidential campaign, according to a person familiar with the matter.
“Good luck Mr. Mustache!” one message sent in August 2021 said, according to a person who described investigative documents.
The FBI and national security lawyers in Maryland, and at Justice Department headquarters, formally opened an investigation into the hack in 2022, sources said. Early in the probe, prosecutors on the investigation got warrants to receive the data from service companies that hosted relevant accounts, such as Yahoo for Bolton’s AOL account and Google for another account, sources said.
The work building a case was slow and meticulous. Information returned to the prosecutors needed to be reviewed by both the intelligence community, which was sensitive to classified information, and processed through a filter team at the Justice Department that would pull out confidential attorney-client records, because Bolton was a lawyer.
For years, the work around what Bolton had and shared in his email account was an investigation essentially walled off from the one related to his book, which had been run by the US Attorney’s office in the District of Columbia.
By the time investigators were ready to obtain a search warrant in August, the book manuscript had once again become part of the case. It was part – along with the hack – of what prosecutors pointed to in court as a basis for searching his office and home, according to court filings.
The decision to search Bolton’s office and especially his home were crucial in the final turn of the investigation before the indictment this week.
While investigators spent months assembling an idea of the emails and classified records they would want to use to build the case, Bolton’s home contained printed copies of some of the emails, the indictment said. Investigators had long suspected they would find hard copies like those, sources told CNN, because some of the emails Bolton wrote to his family he noted were for “the Archives.”

Trump has repeatedly attacked Bolton since the release of his 2020 book and as Bolton has become one of the more prominent ex-Trump staffers turned critic of the president.
Bolton was named Trump’s third national security adviser in 2018, a position that marked the culmination of a lengthy career in Washington across multiple administrations, including as George W. Bush’s ambassador to the United Nations.
The initial Justice Department criminal probe of Bolton began in 2020 with an investigation into whether his he violated the law by including information the administration said was classified in his memoir. The same year, the Trump administration sued in civil court to try to stop publication of Bolton’s book over a dispute of whether he got proper sign off from classification authorities.
Bolton’s memoir included shocking allegations about the inner workings of the Trump White House, including that Trump requested Chinese help to win the 2020 election, argued Venezuela was part of the US and offered to help Turkey’s leader avoid a Justice Department probe.
Trump publicly called for Bolton to be prosecuted in 2020 over the book’s publication, saying in an interview that his former national security advisor released “massive amounts” of classified information in its pages.
“It’s really treasonous what he did,” Trump said at the time.
On X, then called Twitter, Trump called Bolton “a lowlife who should be in jail.”
This year, Trump hasn’t frequently commented this year on the Bolton probe – a stark contrast from his public pressure campaigns for the prosecutions of other political foes who were key figures in investigations into himself.
But since the search of Bolton’s house and office in August, Trump has asked advisers about the status of the case. He had been assured in recent weeks that they were moving ahead and that it was a strong case, sources said.
In late August, when FBI agents executed a search warrants on Bolton’s home and office, they seized electronics and multiple documents labeled “secret,” “confidential,” and “classified,” including some about weapons of mass destruction, according to court records filed by prosecutors.
Bondi, Patel and Deputy FBI Director Dan Bongino all posted statements on X the morning of the search, breaking department norms of not commenting on ongoing investigations.

“Public corruption will not be tolerated,” FBI Deputy Director Dan Bongino wrote.
After the search, Bolton’s attorney Abbe Lowell said that the records Bolton kept would have been typical of those kept by a long-time government official. In a statement Thursday, Lowell said that the records were unclassified, shared only with his immediate family, were known to the FBI and were “personal diaries.”
The next month, senior Justice Department leaders, including an attorney from the deputy attorney general’s office, were pressing for the US Attorney’s office to charge Bolton in the days after Trump complained that prosecutions of his enemies weren’t moving quickly enough.
But prosecutors in the Maryland US attorney’s office pushed back, arguing the timeline was too aggressive and they needed more time to bring a stronger case against Bolton, including reviewing the records obtained from the search warrant.
One Justice Department official was considering pulling prosecutors off the case out of opposition to the deputy attorney general’s instruction.
In the end, though, the political pressure eased on the Maryland office after Comey’s indictment. Career prosecutors on the case withdrew their reservations on timing and set in motion finalizing the indictment last weekend.
On Thursday, the lead prosecutor in Bolton’s case, Thomas Sullivan – who also worked on the Biden classified documents investigation under special counsel Robert Hur – presented to a federal grand jury for a little over two hours at the federal courthouse about 20 minutes outside DC.
Fifteen minutes after members of the grand jury filed out of the courthouse, Sullivan, four of his colleagues and the jury foreperson took an elevator one floor up to Magistrate Judge Gina Simms’ courtroom to deliver the indictments approved that day. After the foreperson handed up the indictments, the judge asked if there were any other matters she needed addressed, to which Sullivan said yes.
He handed the judge a slim red file, but and said nothing else. Simms then quickly reviewed the file – also not saying aloud any details of it – before adjourning. The entire proceeding lasted less than 10 minutes.
Outside the courtroom, Sullivan said few words to reporters seeking information about what he gave the judge.
“I would just stay posted,” he said. “Stay tuned.”
CNN’s Devan Cole contributed to this report.