The Department of Justice’s stunning reversal of its account of what transpired in a Virginia grand jury room could have fateful consequences for both the Trump administration and the future of the former director of the FBI, James Comey.

The interim United States attorney, Lindsey Halligan, now avers in a “Notice Correcting the Record” that the grand jury that charged Mr. Comey with lying to Congress and obstructing a congressional investigation actually saw the entirety of the indictment. That represents a change from Ms. Halligan’s testimony during a hearing on Wednesday, when she represented that the final version of the indictment was not seen by the full complement of jurors.

Ms. Halligan’s filing is directed at the presiding judge, Michael Nachmanoff, an appointee of President Biden. Judge Nachmanoff on Wednesday summoned Ms. Halligan to the stand even though she was not arguing in the hearing, which was devoted to an effort by Mr. Comey to dismiss the case. Mr. Comey’s lawyer, Michael Dreeben — a veteran of the teams assembled by Special Counsel Robert Mueller and Jack Smith — insists that “there is no indictment” and that the charges are void.

Ms. Halligan, who, unusually, secured the charges from the grand jury herself, now argues that the “grand jury voted on —  and true-billed —  the two-count indictment.” She insists that there is “no room for ambiguity.” The validity of the indictment is a high-stakes issue for both sides because the government secured charges against Mr. Comey just five days before the relevant statute of limitations would have barred charges.

That makes it unlikely that charges could be refiled if the case is thrown out for any reason — including, as Mr. Comey argues, “irregularities” in the grand jury process. The confusion in the process appears to stem from how the indictment was procured. Ms. Halligan initially asked the grand jury to indict on three counts. The jurors, — also unusually —  only approved two of the charges. The issue is whether the whole jury saw the indictment’s final form.

Ms. Halligan now says that the jury did. She cites the transcript, which records that the foreperson declared “so the three counts should just be one count. It was the very first count that we did not agree on and the Count Two and Three were then put in a different package, which we agreed on.” The transcript, though, also shows the presiding magistrate judge, Lindsey Vaala, admitting that she was “a little confused as to why I was handed two things with the same case number that are inconsistent.”

Judge Vaala ultimately directed that the two-count indictment be docketed, and it is now the one guiding the government’s case. Both charges relate to testimony that Mr. Comey delivered to Congress in 2020 about leaks with respect to investigations into Russian interference in the 2016 election. Mr. Comey contends that his testimony to Senator Ted Cruz was “literally true,” though the government accuses him of perjury.

Mr. Comey’s team, in any event, is not inclined to let Ms. Halligan backtrack. On Thursday the former director of the FBI filed a memorandum to Judge Nachmanoff informing the jurist, a former public defender, that he is doubling down on his drive to dismiss the prosecution. Mr. Comey writes that the case against him “shocks the conscience” and that the government “did not even present the operative indictment to the grand jury, meaning no indictment was returned before the statute of limitations expired.”

Mr. Comey’s latest memo comes as a request that Judge Nachmanoff order the government to turn over the entire records of the grand jury proceedings. That position has already been endorsed by another magistrate judge, William Fitzpatrick, who lacks the power to order such a dramatic step. Mr. Comey argues that “the government’s concession that it never presented the operative indictment in this case to the grand jury for a vote is a death knell for the government’s case.”

Judge Fitzpatrick accused Ms. Halligan of  “fundamental misstatements of the law.” The judge also reckoned that the “short time span between the moment the prosecutor learned that the grand jury rejected one count in the original indictment and the time the prosecutor appeared in court to return the second indictment could not have been sufficient to draft the second indictment … and give them an opportunity to deliberate and render a decision on the new indictment.”  

The requirement that at least 12 jurors agree is constitutional bedrock. The Fifth Amendment ordains that no “person shall be held to answer for a capital, or otherwise infamous crime, unless on a presentment or indictment of a Grand Jury.” The Federal Rules of Criminal Procedure, which govern trials like Mr. Comey’s mandate that a “grand jury may indict only if at least 12 jurors concur.”