Left: Lindsey Halligan, special assistant to the president, speaks with a reporter outside of the White House, Wednesday, Aug. 20, 2025, in Washington. (AP Photo/Jacquelyn Martin). Right: Former Director of the Federal Bureau of Investigation James Comey gestures while addressing a gathering at Harvard University's Institute of Politics' JFK Jr. Forum in Cambridge, Mass., Monday, Feb. 24, 2020. (AP Photo/Charles Krupa).

On the same day that interim U.S. attorney Lindsey Halligan made a startling admission in open court on exactly how the indictment of ex-FBI Director James Comey came about, the DOJ strenuously opposed a magistrate judge's order to hand over "all" grand jury materials to the defense in light of "profound investigative missteps."

The last-ditch arguments against U.S. Magistrate Judge William Fitzpatrick's order, filed to U.S. District Judge Michael Nachmanoff, stated that even if Halligan made "misstatements of law" to the grand jury, it should not lead to the dismissal of the case.

"The magistrate judge also found that two alleged misstatements of the law by the U.S. Attorney to the grand jury provided another basis for ordering disclosure of the grand jury material," the DOJ said. "That, too, was contrary to law, since those alleged misstatements — even if they were incorrect statements of the law — are no basis to dismiss the indictment."

Arguing that Comey did not carry his "burden" to override grand jury secrecy, the DOJ asserted that Fitzpatrick "made what appear to be a series of effectively preliminary legal rulings and factual findings, pursuant to 'its supervisory authority to dismiss the indictment,' as its basis for ordering disclosure of the grand jury material despite having received neither substantial briefing nor having been presented evidence[.]"

"The Government respectfully submits that doing so was erroneous," the DOJ added.

In a full-throated defense of Halligan, the Trump administration stated that Fitzpatrick misread the grand jury transcript, drew "incorrect legal conclusions" based on "factual assumptions" about her activities.

"The U.S. Attorney did not misstate the law, the grand jury was not misled, and the transcript shows a routine, regular presentation of the indictment," the objections filing concluded. "Because the magistrate's findings are unsupported by the record and inconsistent with the governing legal standards, the Court should set aside the magistrate judge's order and deny the request for disclosure[.]"

On Monday, Fitzpatrick said his in-chambers review of the grand jury materials suggested that Halligan may have compromised the case before the grand jury, warming to the defense argument that some "misconduct" had sullied the obstruction and false statement indictment in the Eastern District of Virginia.

The defense claimed that Halligan's presentation and a potentially "tainted" FBI agent witness who "may have been exposed" to attorney-client privileged information could tear the case apart.

The DOJ vehemently defended the "long-established public interest in grand jury secrecy" but ultimately fell short in Fitzpatrick's eyes.

The magistrate highlighted a "disturbing pattern of profound investigative missteps" in reaching that decision.

Regarding Halligan, the lone signer of the Comey indictment and the only prosecutor in the grand jury room, Fitzpatrick said he "identified two statements" that she made to grand jurors that "on their face appear to be fundamental misstatements of law that could compromise the integrity of the grand jury process."

One of those statements seems to have emphasized that Comey's silence could be used against him, while the other "clearly suggested to the grand jury that they did not have to rely only on the record before them to determine probable cause but could be assured the government had more evidence–perhaps better evidence–that would be presented at trial," Fitzpatrick said.

"[T]he prosecutor made statements to the grand jurors that could reasonably form the basis for the defense to challenge whether the grand jury proceedings were infected with constitutional error," he said.

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The magistrate also identified another issue that came up again on Wednesday.

Fitzpatrick noted that it appeared the two-count Comey indictment, solely signed by Halligan, was not actually presented to the full grand jury after count one, a false statement charge, in the initial three-count indictment, failed.

The magistrate said it seemed he was in "uncharted legal territory" because the DOJ, rather than presenting a new two-count indictment before the grand jury, removed the no-billed count and had the foreperson sign the substitute document that differed from the one the full grand jury actually deliberated on.

"The second indictment was a new indictment and therefore the undersigned concluded after reviewing the grand jury transcript that the prosecutor would have presented the second indictment to the grand jury for consideration before it was returned in open court. It now appears that may not have happened," he said. "If this procedure did not take place, then the Court is in uncharted legal territory in that the indictment returned in open court was not the same charging document presented to and deliberated upon by the grand jury."

"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," Fitzpatrick added.

After Fitzpatrick ordered the grand jury materials to be shared with Comey's team right away, the DOJ swiftly filed an emergency motion for a stay and got one, leading to the Wednesday by 5 p.m. objections filing deadline.

Earlier on Wednesday, Comey's defense was in court to argue the indictment should be tossed out on vindictive and selective prosecution grounds.

At one point of the proceeding, over which Nachmanoff presided, Halligan's brief testimony in open court shocked court watchers.

According to reporters who were there, Halligan acknowledged that the full grand jury wasn't presented or shown the "operative" two-count indictment she signed and submitted.

HUGE development IN hearing for Comey selective prosecution motion, It turns out that the grand jury NEVER saw the operative indictment. Whole separate basis for dismissal. Standby for more.

— Harry Litman (@harrylitman.bsky.social) November 19, 2025 at 11:27 AM

OMFG

Did Halligan just gin up a new second indictment, sign it, and present it to the judge???[image or embed]— Katie Phang (@katiephang.bsky.social) November 19, 2025 at 12:00 PM

Comey's team said that procedural error admission meant "no indictment was returned" because there was no vote, according to CNN.