The Trump administration has recently sought to clarify concerns surrounding an alleged gap in the transcript from the grand jury proceedings that led to the indictment of former FBI Director James Comey. This clarification came in response to critical observations made by a federal judge regarding the integrity of the transcription process.

In a series of legal documents filed on Friday, the U.S. Department of Justice, along with U.S. Attorney General Pam Bondi and Lindsey Halligan, defended the accuracy of the transcript, dismissing allegations of any missing sections. Despite these assurances, questions remain about the completeness of the document.

Earlier in the week, Senior U.S. District Judge Cameron McGowan Currie, appointed by former President Bill Clinton, highlighted the issue, suggesting potential irregularities that have put the Department of Justice in a challenging position. This scrutiny has intensified ongoing discussions about the legitimacy of Halligan’s appointment as interim U.S. attorney.

During a Thursday court hearing concerning Halligan’s controversial appointment, Judge Currie pointed out that a crucial segment of the grand jury transcript seemed absent. Notably, the judge remarked on the lack of a court reporter’s presence or activity during a critical part of the proceedings on September 25. This gap was noted to occur from approximately 4:30 p.m. until the grand jury returned the indictment against Comey, extending beyond standard office hours, as previously reported by Law&Crime.

During a hearing over the appointment battle on Thursday, Currie described a portion of the transcript as “missing.” The judge said it “appears there was no court reporter present” or the court reporter had ceased activity during the grand jury proceeding from roughly 4:30 p.m. until the Comey indictment was handed up past normal business hours on Sept. 25, as Law&Crime previously reported.

“It became obvious to me,” the judge said during the hearing, that Bondi “could not have reviewed” the whole grand jury proceeding.

The salience of such a review is due to Bondi’s retroactive ratification of Halligan’s work on both the case against Comey as well as the indictment filed against New York Attorney General Letitia James.

In an appointment order filed Nov. 3, dated Oct. 31, Bondi said she appointed Halligan as U.S. attorney for the Eastern District of Virginia on Sept. 22. The order also says Halligan was simultaneously made a “Special Attorney,” which authorizes her to “conduct and supervise the prosecutions” of Comey and James. Finally, the order aims to specifically “ratify” Halligan’s “actions before the grand jury and her signature on the indictments returned by the grand jury in each case.”

To hear Comey’s attorney Ephraim McDowell tell it, Halligan’s would-be appointment represents “a fundamental defect” showing she had “no authority” to present the case to the grand jury on her own. It was “evasion of the Appointments Clause and separation of powers,” according to a courtroom report by CNN.

An attorney for James echoed that assessment. Abbe Lowell said the government is claiming the power to authorize virtually anyone to “go into a grand jury and get an indictment and the attorney general could later authorize that.” To that end, Lowell said Halligan is “pretending” to be a U.S. attorney, and cannot, by law, prosecute the cases.

The government, for its part, pushed back on the timeline issue. Currie responded by noting how days after the retroactive ratification, the DOJ came up with more grand jury details it didn’t have earlier.

The judge seemed to frame the issue of the “missing” grand jury minutes as perhaps somehow indicative of – or at least related to – the alleged underlying problem with Halligan’s appointment.

The DOJ seemingly sensed as much in the six different documents intended to address and correct the issue docketed late Friday.

First, the government filed an “informative notice correcting the record,” which described the issue and asked the court to “take notice of the attached declaration of U.S. Attorney Lindsey Halligan (Exhibit 1), and the attached ratification dated November 14, 2025, by U.S. Attorney General Pamela Bondi (Exhibit 2).”

The first exhibit refers to the “alleged gap in the grand-jury record” and says “the transcript reflects that I, Lindsey Halligan and the court reporter exited the grand-jury room.”

The filing offers to “clarify the precise sequence of events” that occurred on Sept. 22, and says the allegedly missing time was simply accounting for the deliberations of the grand jurors.

“By identifying that specific timeframe, the court placed the timing of the proceedings in dispute,” the document reads. “There are no missing minutes, contrary to the suggestion raised by the court.”

Left to right: the docket showing a correction of the clarification notice; a typo in one of Halligan’s filings (DOJ).

The second exhibit is an additional retroactive ratification of Halligan’s authority. This time, Bondi makes pains to reference the entirety of the grand jury proceedings and aims to refute the court’s suggestion that the appointment was improper due to the missing minutes.

Bondi’s second retroactive ratification reads, in full:

On October 31, 2025, and based on the record of the grand jury proceedings that was available to the government at the time, I ratified the actions of United States Attorney Lindsey Halligan before the grand jury and her signature on the indictment returned by the grand jury in the case of United States v. Comey (Case No. 1:25-CR-00272). See Att’y Gen. Order No. 6485- 2025. The district court has subsequently raised questions about the completeness of the record of the grand jury proceedings presented to me at the time of that initial ratification. For the avoidance of doubt, I have reviewed the entirety of the record now available to the government and confirm my knowledge of the material facts associated with the grand jury proceedings. Based on that knowledge, I hereby exercise the authority vested in the Attorney General by law, including 28 U.S.C. § 509, 510, and 518(b), to ratify Ms. Halligan’s actions before the grand jury and her signature on the indictment returned by the grand jury.

The DOJ’s attempted cleanup, however, took a couple of tries.

In short order, the trio of documents was swiftly re-filed due to a typo. In the first exhibit of the original suite of clarification documents, Halligan was listed as “Interim United Stated Attorney.”