On the same day that interim U.S. Attorney Lindsey Halligan made a surprising revelation in court regarding the indictment process of former FBI Director James Comey, the Department of Justice (DOJ) strongly opposed a magistrate judge’s order. The order required the DOJ to release all grand jury materials to the defense due to “significant investigative errors.”

The DOJ’s last-minute objections were submitted to U.S. District Judge Michael Nachmanoff. These objections argued that even if Halligan had made “misstatements of law” during grand jury proceedings, these should not warrant the case’s dismissal.

The DOJ stated, “The magistrate judge also found that two alleged misstatements of the law by the U.S. Attorney to the grand jury justified the disclosure of the grand jury materials. This, however, was contrary to law, as such alleged misstatements—despite being incorrect—do not constitute grounds for dismissing the indictment.”

Contending that Comey failed to meet his “burden” to breach grand jury confidentiality, the DOJ argued that Judge Fitzpatrick made provisional legal rulings and factual determinations without substantial briefing or evidence, using these as a basis for ordering the disclosure of the grand jury materials.

The DOJ further commented, “The Government respectfully submits that this approach was erroneous.”

Defending Halligan, the Trump administration accused Judge Fitzpatrick of misinterpreting the grand jury transcript and drawing “incorrect legal conclusions” based on “factual assumptions” about Halligan’s conduct.

“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.

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.

Lindsey Halligan should be immediately disbarred. https://t.co/DUDeJ5gBFp

— Anthony Michael Kreis (@AnthonyMKreis) November 19, 2025

Hearing in Comey just ended. Govt admits 2d indictment never presented to full grand jury. Judge concerned. AUSA also admits DAG Blanche’s office told him not to disclose whether earlier prosecutors wrote a declination memo (saying why there was no case).

— Roger Parloff (@rparloff) November 19, 2025

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???

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— 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.