You ever get the sense Donald Trump and John Bolton might not like each other? 

Bolton, who served as National Security Advisor in the first Trump administration, has publicly called the President “a danger for the republic,” “stunningly uninformed,” and “unfit for office.” Trump, in turn, has branded Bolton “a sleazebag, actually,” “a very dumb person,” and the owner of a “stupid white moustache.” Upon publication of Bolton’s 2020 tell-all book, Trump responded, “I believe that he’s a criminal, and I believe, frankly, he should go to jail for that.” 

Trump might get his wish. While Bolton resides firmly on Trump’s enemies list, the indictment returned against him Thursday in federal district court in Maryland also bears substantial hallmarks of legitimacy. Trump surely takes retributive delight in Bolton’s prosecution, and has encouraged it in unsubtle ways. At the same time, the Bolton indictment appears to have genuine merit. 

The indictment charges Bolton with eighteen federal crimes: eight related to transmitting sensitive national defense information and ten more for improperly retaining the same. The information at issue contained deadly serious government secrets. Bolton allegedly disclosed to outsiders information about “future attack” plans by foreign adversary groups; details of impending missile launches by foreign adversaries; information about sensitive intelligence sources; and assessments about leaders of foreign countries. Apparently, Bolton would type up notes based on information he learned as National Security Advisor. He’d then use his personal AOL account (which was eventually hacked by Iran) to email “diary-like entries” to two people – both relatives of his – who had no security clearances. Bolton also allegedly kept highly sensitive documents in his private home.  

There’s no doubt that Bolton, a onetime U.S. ambassador and National Security Advisor, was well aware of the rules governing handling of classified information. As the indictment notes, he said publicly in 2017, “If you’re conscious of the need to protect classified information you’ll remember what the rules are. If I had done at the State Department what Hillary Clinton did, I’d be wearing an orange jumpsuit now.” More recently, in 2025, Bolton railed against various public officials who committed the “original sin” (as Bolton then phrased it) of communicating about sensitive national security matters over the Signal app. The legal takeaway: A defense of ignorance or lack of intent won’t fly. 

Bolton, through his attorney, categorically denies wrongdoing.

While we now have a clear sense of the prosecution’s theory of criminality, we don’t yet have a definitive read on the strength of the proof, or on Bolton’s defense. That’ll come in time, as the Justice Department turns over discovery to the defense, as the parties file motions in court, and eventually when the case goes to trial. 

But for now, we can look at a series of reliable collateral indicators that suggest this prosecution is legitimate. Consider, first, that the Justice Department’s instant investigation of Bolton reportedly escalated during the Biden administration. Trump surely was delighted to find it waiting for him when he took office, but – unlike the cases against James Comey and Letitia James – this one wasn’t originated by the President and his band of gleeful political enforcers. 

It also appears that the Bolton matter arose organically, and not because some official decided to root around for dirt buried in the mortgage files of a disfavored subject. According to public reporting and court documents filed in connection with search warrants conducted at Bolton’s home and office in August, the criminal inquiry began when U.S. intelligence officials learned that Bolton’s AOL email account had been hacked by a foreign government. The New York Times reported that those emails contained “sensitive information that Mr. Bolton, while still working in the first Trump administration, appeared to have sent to people close to him on an unclassified system.” (The indictment confirms this). The case arose, then, in the ordinary course of intelligence and law enforcement business, and not as a targeted inquiry aimed at Bolton. 

We also know that career, nonpolitical DOJ prosecutors at one point sought more time to review the evidence against Bolton, and now are on board with a prosecution. Again, note the contrast to the Comey and James indictments, which prompted a string of resignations by (and terminations of) dissenting prosecutorial professionals who saw no good faith basis to indict. 

Prosecutors are hardly alone in concluding that substantial evidence exists to establish that Bolton committed a crime. Before the Justice Department executed search warrants at Bolton’s Maryland home and Washington, D.C. office in August, prosecutors had to obtain authorization from two federal judges (one in each jurisdiction). We know, as a matter of law, that those judges concluded that prosecutors established at least probable cause that a crime had been committed and that the searches would likely uncover evidence of that crime. And we know that a grand jury heard the evidence and found probable cause to issue the indictment. 

The probable cause standard is, of course, lower than the “beyond a reasonable doubt” burden that prosecutors must ultimately satisfy at trial. But it’s not nothing, either. I can attest from experience that, while grand juries can be pushovers, judges do scrutinize search warrant applications fairly closely – particularly if the target is a high-profile former public official. 

Nor can Bolton claim differential treatment, given other semi-recent cases involving potential mishandling of classified information. After Hillary Clinton used a private email server as Secretary of State, she became the subject of a prolonged criminal investigation that culminated with a 2016 election-eve public announcement by the FBI director – the aforementioned Comey, as history remembers  – that she had been “extremely careless” but would not be indicted. When the public learned that Joe Biden kept classified documents at his private home and office, the Justice Department (under Biden himself) appointed a special counsel, Robert Hur, who investigated for over a year and concluded in early 2024 Biden had “willfully retained and disclosed classified materials” but, on balance, should not be charged. And when Trump took classified documents to Mar-A-Lago, he got indicted by DOJ special counsel Jack Smith. That case could’ve landed Trump in prison, had he not won the 2024 election. Bolton’s conduct, if proved, is more serious than all of those recent examples – especially given his systematic and intentional dissemination of the government’s most sensitive secrets to two outsiders. 

There’s no question Trump despises Bolton (and vice versa). And Trump plainly has been giddy at the prospect of Bolton’s indictment. But the Bolton case appears to differ in kind from the recent prosecutions of Comey and James. This one relates to far more serious conduct, and it arose under less dubious circumstances. Ultimately this is a problem Trump has created with his payback spree: It’s increasingly hard to tell the bogus cases against his political antagonists from the valid ones.