ALEXANDRIA, VA—In a stunning admission, prosecutors in the James Comey case conceded that the two-count indictment against the former FBI director was never presented to or voted on by a grand jury. 

The paperwork snafu that has bedeviled the case from the beginning came into much sharper focus after persistent questioning from U.S. District Judge Michael Nachmanoff in federal court Wednesday in Alexandria, Virginia.

At issue is whether U.S. Attorney Lindsey Halligan — an insurance lawyer with no prior prosecutorial experience — followed proper procedure after the grand jury rejected count 1 of the original proposed indictment it was given.

The prosecutors in the case on Wednesday for a time turned into witnesses as the judge pressed them for details on what had happened in the late afternoon of Sept 25, 2025. After extensive back and forth, including hauling Halligan herself to the podium (she has not spoken in any substantive way in open court in the case before today), prosecutors conceded that the draft of the operative two-count second indictment that the case has been proceeding based on was never presented to nor voted on by the grand jury.

Instead, Halligan and the grand jury foreman and another grand juror presented both the rejected indictment and the revised indictment to a magistrate judge, who noted some of the incongruities and tried to clean up the mess. Different ink used on the two indictments was among the early clues that things might be amiss, and Nachmanoff noted the ink disparity in court today.

What was on open question until today was whether the grand jury as a whole had ever considered the revised version of the indictment. Ironically, the issue was resurfaced again by Halligan herself on Friday, when she filed a declaration in the case saying she had had no further contact with the grand jury after presenting it with the original three-count indictment. The declaration was filed in response to concerns raised by another judge considering Comey’s challenge to the validity of Halligan’s appointment as U.S. attorney, but it caught the eye of Nachmanoff.

The stunning courtroom disclosure — cinematic in its intensity — came in a hearing ostensibly to hear Comey’s motion to dismiss the case on the grounds that it is a vindictive and selective prosecution. That portion of the hearing went very poorly for the government, too, but it was overshadowed by the revelation that there may have been no indictment at all.

As prosecutor Nathaniel Lemons concluded his argument against Comey’s motion to dismiss, Nachmanoff drew him back to podium for a series of questions about the circumstances around the presentation of the indictment to the grand jury.

“What I’m trying to understand is when the second indictment was drafted and when it was presented to the grand jury,” the judge said.

Lemons described a process where Halligan presented the initial indictment and left the grand jury alone while it deliberated. About two hours later, Halligan’s office got word that the grand jury has rejected count 1 but had accepted counts 2 and 3. Someone in her office drafted a revised two-count indictment and handed it to Halligan and that draft went straight to the court, Lemons said.

Nachmanoff asked again if the second indictment was ever presented to the grand jury. Lemons conferred with Halligan for a moment before saying, “The government’s understanding is only one indictment was presented.”

Nachmanoff tried a third time to pin down whether the grand jury had ever seen the second indictment: “It’s a document that was never shown to the grand jury or presented in the grand jury room?”

“Correct, that’s my understanding,” Lemons said.

Nachmanoff seemed baffled by the admission.

At that point, Nachmanoff tired of Lemons playing intermediary and summoned Halligan to the podium to ask if any grand jurors other than the foreman were present in court when the indictment was given to duty judge. A very defensive Halligan said one other juror was present, then began reciting what the duty judge had said. Nachmanoff cut her off. “I’m familiar with the transcript,” he said. “You may sit down.”

Nachmanoff ordered the parties to brief him immediately on the implications of the revelations that the indictment may not be legitimate. In particular, he pointed them to a 1969 case from the D.C. Circuit Court of Appeals. 

The implications of the apparent screw up aren’t immediately clear, but they are potentially catastrophic to the government’s case. The statute of limitations on the charges against Comey expired shortly after the purported indictment was secured. So if the case against Comey is dismissed — or, more precisely, if the case never existed — then the government may not be able to refile charges against him.

A ruling Monday by yet a third judge involved in the Comey case raised the prospect of the second indictment having bypassed the grand jury and warned it would be “unchartered legal territory.”

“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,” magistrate Judge William Fitzpatrick wrote as he ordered the government to turn over grand jury transcripts and recordings to Comey.