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The Justice Department engaged in a “disturbing pattern of profound investigative missteps” in the process of securing an indictment against former FBI Director James Comey, a federal judge ruled Monday in directing prosecutors to provide defense lawyers with all grand jury materials from the case.

Those problems, wrote Magistrate Judge William Fitzpatrick, include “fundamental misstatements of the law” by a prosecutor to the grand jury that indicted Comey in September, the use of potentially privileged communications during the investigation and unexplained irregularities in the transcript of the grand jury proceedings.

“The Court recognizes that the relief sought by the defense is rarely granted,” Fitzpatrick wrote “However, the record points to a disturbing pattern of profound investigative missteps, missteps that led an FBI agent and a prosecutor to potentially undermine the integrity of the grand jury proceeding.”

The 24-page opinion is the most blistering assessment yet by a judge of the Justice Department’s actions leading up to the Comey indictment. It underscores how procedural missteps and prosecutorial inexperience have combined to imperil the prosecution pushed by President Donald Trump for reasons separate and apart from the substance of the disputed allegations against Comey.

The Comey case and a separate prosecution of New York Attorney General Letitia James have hastened concerns that the Justice Department is being weaponized in pursuit of Trump’s political opponents. Both defendants have filed multiple motions to dismiss the cases against them before trial, arguing that the prosecutions are improperly vindictive and that the prosecutor who filed the charges, Lindsey Halligan, was illegally appointed.

A different judge is set to decide by Thanksgiving on the challenges by Comey and James to Halligan’s appointment.

Though grand jury proceedings are presumptively secret, Comey’s lawyers had sought records from the process out of concern that irregularities may have tainted the case. The sole prosecutor who defense lawyers say presented the case to the grand jury was Halligan, a former White House aide with no prior prosecutorial experience who was appointed just days before the indictment to the job of interim U.S. attorney for the Eastern District of Virginia.

In his order Monday, Fitzpatrick said that after reviewing the grand jury transcript himself, he had come away deeply concerned about the integrity of the case.

“Here, the procedural and substantive irregularities that occurred before the grand jury, and the manner in which evidence presented to the grand jury was collected and used, may rise to the level of government misconduct resulting in prejudice to Mr. Comey,” Fitzpatrick said.

The Justice Department responded to the ruling by asking that it be put on hold to give prosecutors time to file objections. The government said it believed Fitzpatrick “may have misinterpreted” some facts in issuing his ruling.

Fitzpatrick listed, among nearly a dozen irregularities in his ruling, two different comments that a prosecutor — presumably, Halligan — made to the grand jury that he said represented “fundamental misstatements of the law.”

The actual statements are blacked out, but Fitzpatrick said the prosecutor seems to have ignored the fact that a grand jury may not draw a negative inference about a person who exercises his right not to testify in front of it. He said she also appeared to suggest to grand jurors that they did not need to rely only on what was presented to them and could instead before assured that there was additional evidence that would be presented at trial.

The judge also drew attention to the jumbled manner in which the indictment was obtained and indicated that a transcript and recording of the proceedings do not provide a full account of what occurred. Halligan initially sought a three-count indictment of Comey, but after the grand jury rejected one of the three proposed counts and found probable cause to indict on the other two counts, a second two-count indictment was prepared and signed.

But Fitzpatrick said it was not clear to him in reviewing the record that the indictment that Halligan presented in court at the conclusion of the process had been presented to the grand jury for their deliberation.

“Either way, this unusual series of events, still not fully explained by the prosecutor’s declaration, calls into question the presumption of regularity generally associated with grand jury proceedings, and provides another genuine issue the defense may raise to challenge the manner in which the government obtained the indictment,” he wrote.

The two-count indictment charges Comey with lying to Congress in September 2020 when he suggested under questioning that he had not authorized FBI leaks of information to the news media. His lawyers say the question he was responding to was vague and confusing but the answer he gave to the Senate Judiciary Committee was true.

The line of questioning from Sen. Ted Cruz appeared to focus on whether Comey had authorized his former deputy director, Andrew McCabe, to speak with the news media. But since the indictment, prosecutors have made clear that their indictment centers on allegations that Comey permitted a separate person — a close friend and Columbia University law professor, Dan Richman — to serve as an anonymous source in interactions with reporters.

The FBI executed search warrants in 2019 and 2020 to access messages between Richman and Comey as part of a media leaks investigation that did not result in charges. But Fitzpatrick said he was concerned that communications between the men that might have been protected by attorney-client privilege — Richman was at one point functioning as a lawyer for Comey — were exposed to the grand jury without Comey having had an opportunity to object.