A federal judge has delivered a scathing rebuke to the Justice Department over its handling of the case against former FBI Director James Comey, citing “a disturbing pattern of profound investigative missteps” that may have compromised the integrity of the grand jury process.

In a 24-page opinion issued Monday, Magistrate Judge William Fitzpatrick ordered prosecutors to provide Comey’s defense team with all grand jury materials from the case—a rare move that underscores the severity of the procedural violations identified by the court.

“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,” Fitzpatrick wrote, delivering the most blistering judicial assessment yet of the Justice Department’s actions in the Comey case.

The ruling highlights multiple concerns about the case, which has fueled broader allegations that the Justice Department is being weaponized against political opponents of President Donald Trump. The judge identified nearly a dozen irregularities in the grand jury process, including what he called “fundamental misstatements of the law” by the prosecutor to the grand jury.

Among the issues cited was the prosecutor’s apparent failure to respect a defendant’s right not to testify before a grand jury without negative inference. The judge also noted that the prosecutor seemed to suggest to grand jurors that they didn’t need to rely solely on presented evidence, implying additional evidence would emerge at trial.

Comey was indicted in September on two counts of lying to Congress during 2020 testimony before the Senate Judiciary Committee. The charges allege he falsely stated he had not authorized FBI leaks to the news media. His defense team maintains the question posed by Senator Ted Cruz was vague and confusing, and that Comey’s answer was truthful.

The case has been further complicated by questions surrounding Lindsey Halligan, the prosecutor who presented the case to the grand jury. Halligan, a former White House aide with no prior prosecutorial experience, was appointed interim U.S. Attorney for the Eastern District of Virginia just days before securing the indictment against Comey.

Both Comey and New York Attorney General Letitia James—who faces a separate prosecution—have filed motions to dismiss their cases, arguing that Halligan was illegally appointed and that the prosecutions are improperly vindictive. A different judge is expected to rule on these challenges by Thanksgiving.

Judge Fitzpatrick also expressed concern about the “jumbled manner” in which the indictment was obtained. Initially, Halligan sought a three-count indictment, but the grand jury rejected one count while finding probable cause for the other two. A second, two-count indictment was then prepared and signed, but the judge questioned whether this final version was actually presented to the grand jury for deliberation.

“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,” Fitzpatrick wrote.

Another significant issue identified by the court involves potentially privileged communications between Comey and Columbia University law professor Dan Richman, who prosecutors allege served as an anonymous source for media contacts at Comey’s direction. The FBI seized messages between Comey and Richman through search warrants in 2019 and 2020, but the judge noted that these communications might have been protected by attorney-client privilege, as Richman had at one point functioned as Comey’s lawyer.

The Justice Department has responded to the ruling by asking for a stay, arguing that Fitzpatrick “may have misinterpreted” some facts in issuing his decision. The department seeks time to file formal objections.

This judicial rebuke comes at a critical juncture for the Justice Department, as concerns about politicization have intensified public scrutiny of high-profile prosecutions involving figures connected to former President Trump or his political rivals.