Lawyers for James B. Comey, the former F.B.I. director, asked a federal judge on Friday evening to throw out the charges he was facing because the inexperienced prosecutor picked by President Trump to bring the case failed to secure the approval of the full grand jury that purportedly returned the indictment against him.
The request to dismiss the case was contained in a motion filed in Federal District Court in Alexandria, Va., two days after the prosecutor, Lindsey Halligan, acknowledged at a tense court hearing that she had never shown a second — and final — version of the indictment of Mr. Comey to the entire grand jury for a vote.
It also came after a magistrate judge involved in Mr. Comey’s case this week issued a blistering ruling detailing “a disturbing pattern of profound investigative missteps” and potential prosecutorial misconduct that undermined “the integrity of the grand jury proceeding.”
The request by Mr. Comey’s legal team was the most significant effort yet to seize on Ms. Halligan’s slapdash presentation to the grand jury as a way of killing the case. Three separate judges involved in hearing the charges against Mr. Comey have all expressed doubts about how she presented evidence to the grand jurors.
It caught the courtroom by surprise on Wednesday morning when Ms. Halligan, the U.S. attorney for the Eastern District of Virginia, and one of her subordinates told Judge Michael S. Nachmanoff, who is overseeing the case, that prosecutors never showed the revised indictment in the case — the one that was ultimately used to charge Mr. Comey — to all of the grand jurors who should have had a chance to approve it.
Ms. Halligan, a former insurance lawyer who had never worked on a criminal case before Mr. Comey’s, went into the grand jury shortly after 2 p.m. on Sept. 25 — by herself and for the very first time — and asked the jurors to return an indictment charging Mr. Comey with three counts, one of which was ultimately rejected.
Typically, a prosecutor in that position would correct the charging document to reflect the split decision, then return to the grand jury to present the case again and secure a second, confirmatory vote.
Prosecutors admitted to Judge Nachmanoff this week that instead of seeking that second vote, Ms. Halligan’s subordinates simply redrafted the indictment, stripping out one count and resubmitting the amended version without time for further explanation or deliberation.
They did so, prosecutors said, not to the full grand jury, but to only the foreperson and her deputy.
All of this confused the magistrate judge, Lindsey R. Vaala, who was on duty that day and took the bench near 7 p.m. expecting to receive an indictment of Mr. Comey. Judge Vaala appeared perplexed when she was handed two indictments — both of them signed by Ms. Halligan and the grand jury foreperson.
“This has never happened before,” Judge Vaala said. “I’ve been handed two documents that are in the Mr. Comey case that are inconsistent with one another. There seems to be a discrepancy.”
When Judge Vaala asked what had happened, Ms. Halligan said she had never seen the failed three-count indictment — only the successful one containing two counts. That assertion caused even more bewilderment.
“It has your signature on it,” Judge Valla said of the first failed indictment.
Complicating matters, Ms. Halligan made an abrupt about-face on Thursday, one day after acknowledging that she had never shown the grand jury the revised indictment. In court papers, she asserted there was conclusive evidence that all the grand jurors had in fact voted on Mr. Comey’s charges.
The proof, the papers said, appeared in the remarks the grand jury foreperson had made in front of Judge Vaala, confirming that she and her colleagues had approved the final, two-count version of the indictment. There was just one problem with the foreperson’s apparently exonerating statements: It was far from clear that she had understood what actually should have happened in the grand jury room any better than Ms. Halligan.
Mr. Comey’s lawyers argued in their Friday evening filing that the foreperson’s assertion was “ambiguous.”
“It could have meant that the grand jury voted to approve a new two-count indictment, or it could have meant that the grand jury voted to approve counts two and three of the original indictment,” they wrote.
If they voted to approve the original counts two and three, it would appear that no one from the government had followed standard procedure by presenting the revised indictment for reconsideration. And they voted to approve a new two-count indictment, there were additional problems, given that the full grand jury transcripts have no record of any prosecutor returning to the grand jury room to speak with the grand jurors.
Mr. Comey stands accused of lying to and obstructing Congress during testimony before the Senate Judiciary Committee in September 2020. At the hearing, he was asked about whether he had authorized anyone at the F.B.I. to serve as an anonymous source in newspaper articles about sensitive political investigations.
As part of their efforts to have the case dismissed, Mr. Comey’s lawyers are seeking to obtain the full set of the transcripts from Ms. Halligan’s grand jury presentation. That is taking place in a separate strand of litigation from their motion to dismiss the case, and could be decided as early as next week.
The lawyers have also filed an array of other legal attacks on the indictment, including one challenging the underlying lawfulness of Ms. Halligan’s appointment as U.S. attorney, and another accusing the Justice Department of having brought the case on Mr. Trump’s behalf as an illegal act of vindictive retribution.
Alan Feuer covers extremism and political violence for The Times, focusing on the criminal cases involving the Jan. 6 attack on the Capitol and against former President Donald J. Trump.
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