The Department of Justice (DOJ) has been singled out for a stinging attack by a federal judge who has accused it of displaying a “disturbing pattern of profound investigative missteps” in its case against former FBI director James B. Comey. This raises the prospect that the prosecution was tainted by a decade old feud leading to government misconduct.

U.S. Magistrate Judge William Fitzpatrick’s 24-page order reads like an indictment of the department’s own conduct. He faulted prosecutors for misrepresenting the law before a grand jury, relying on improperly obtained evidence, and permitting compromised witnesses to testify. The cumulative effect, he wrote, “may rise to the level of government misconduct resulting in prejudice to Mr. Comey.”

The ruling marks the most detailed look yet at what has been a rushed and controversial push by the Trump administration—a second-term administration that has increasingly treated Comey as a symbol of its grievances—to bring charges against the former FBI director.

Late Monday, November 17, U.S. District Judge Michael Nachmanoff paused Fitzpatrick’s order to hand over full grand-jury transcripts, giving the Justice Department time to appeal. But the magistrate judge’s language signals deep judicial unease with a prosecution already overshadowed by political history.

A Feud That Never Ended

The Comey–Trump relationship has defined much of the U.S. political and institutional debate since 2016. As FBI director, Comey became a household name for his handling of the Hillary Clinton email investigation. His decision to sharply criticize Clinton’s “extremely careless” use of a private server—while recommending no charges—angered Democrats. His announcement, just 11 days before the election, that the bureau was reopening the inquiry after discovering additional emails may have shifted political momentum at a critical moment. Clinton later said that move played a significant role in her defeat.

Trump, however, saw Comey’s earlier refusal to charge Clinton as proof the FBI was protecting Democrats. Once in office, the newly inaugurated president privately demanded “loyalty” from Comey during an Oval Office dinner—an account Trump denied but which Comey said reflected inappropriate presidential pressure.

When Comey refused to publicly clear Trump in the Russia investigation, Trump fired him in May 2017.

Comey’s subsequent release—through a friend—of contemporaneous memos documenting his interactions with Trump triggered the appointment of Special Counsel Robert Mueller, deepening the president’s animosity.

That bitterness still animates both sides. When Trump returned to the White House after his 2024 reelection, Comey became one of several longtime critics—along with New York Attorney General Letitia James and Federal Reserve Governor Lisa Cook—who suddenly found themselves in the crosshairs of federal investigations.

DOJ Under Fire

Fitzpatrick’s blistering opinion focuses primarily on the process by which prosecutors charged Comey with lying to Congress about whether he authorized a friend, Columbia University law professor Daniel Richman, to serve as an anonymous media source during the Trump-Russia saga.

The magistrate judge said Lindsey Halligan—the Trump-appointed interim U.S. attorney who presented the case to the grand jury—made “fundamental misstatements of the law,” suggested Comey would have to prove his innocence at trial, and implied that jurors could rely on “better evidence” prosecutors hoped to uncover later. All of that, he said, misstated the government’s burden and misled the grand jury.

Halligan, a former White House aide with no prior prosecutorial experience, took the case to the grand jury after career prosecutors reportedly concluded the evidence was insufficient. She secured an indictment in late September—just before the statute of limitations expired.

Fitzpatrick also questioned whether prosecutors violated Fourth Amendment limits by relying on material seized years earlier from Richman in a separate investigation that ended without charges. Typically, the government must obtain new warrants to re-review such files; Fitzpatrick said it did not.

The judge highlighted another irregularity: the FBI agent who testified before the grand jury had acknowledged accidentally reviewing privileged or sensitive material that should have disqualified him from the investigation. Allowing him to testify was “a radical departure from past DOJ practice,” Fitzpatrick wrote.

The judge even suggested that the indictment publicly returned in open court may not match what the grand jury actually reviewed—a potential procedural breakdown with no clear precedent.

“These are not mere technicalities,” said one former federal prosecutor, noting that courts treat grand-jury integrity as sacrosanct. “If the judge thinks the foundation is compromised, the case may collapse.”

Pam Bondi Enters the Picture

Attorney General Pam Bondi—appointed by Trump in his second term and a longtime political ally—finds herself central to the department’s broader posture. Critics say Bondi has presided over a pattern of targeted investigations against individuals Trump views as adversaries.

Bondi has denied any political motive, insisting she is enforcing federal law with “equal vigor and fairness.” Still, the Comey, James, and Cook investigations have drawn increasing scrutiny, especially as they rely on Halligan, whose independence and qualifications have been repeatedly questioned.

In Georgia, lawyers for Fed Governor Lisa Cook have appealed to Bondi to shut down what they describe as a baseless mortgage-fraud probe. The Supreme Court has already blocked Trump’s attempt to fire Cook from the Federal Reserve, calling the action potentially unlawful.

Meanwhile, lawyers for New York AG Letitia James cited “outrageous government conduct” in their own filings Monday, pointing to alleged misconduct by Bill Pulte, the Federal Housing Finance Agency director pushing mortgage-fraud claims against James. Pulte recently fired internal investigators who were examining whether he had improperly accessed records in pursuit of political targets.

Comey’s Defense and the Stakes Ahead

Comey has fought the charges on multiple fronts. He argues that any grand-jury irregularities alone warrant dismissal. He also says Halligan’s appointment was unlawful, that privileged materials were improperly accessed, and that the case is an unconstitutional extension of Trump’s personal vendetta.

His legal team has drawn parallels to past instances in which courts dismissed prosecutions over government misconduct—notably the botched Ted Stevens case in 2009.

Behind the legal maneuvers lies a broader narrative: a former FBI director long criticized for his role in the Clinton email saga now accusing the government of violating basic constitutional safeguards.

For Comey, the irony is inescapable. He has spent years defending his 2016 actions as an attempt to protect the bureau’s credibility, even if the timing unintentionally reshaped the presidential race. Now he argues that the DOJ has undermined its own credibility in pursuit of him.

A Test of the Justice System’s Integrity

The Comey case has become a test not only of prosecutorial conduct but of whether the Justice Department can function independently of political pressure under a president who has openly demanded prosecutions of rivals.

If Fitzpatrick’s findings hold, the department may face one of the most significant institutional rebukes since the Watergate era—at a moment when its impartiality is already under intense national scrutiny.

For now, Judge Nachmanoff’s temporary stay buys DOJ time. But the magistrate judge’s ruling has shifted momentum sharply toward Comey, raising the possibility that the case—born of a decade-long political feud—may fail not for lack of evidence, but for a failure to uphold the standards that underpin federal justice itself.

Disclaimer: The opinions and views expressed in this article/column are those of the author(s) and do not necessarily reflect the views or positions of South Asian Herald.

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