The prosecution of former FBI Director James Comey encountered significant challenges on Wednesday as the Justice Department admitted to potential issues in how the case was presented to a federal grand jury. This development raises further questions about a politically sensitive case that has already faced multiple challenges and calls for dismissal.

During a court hearing, Comey’s attorneys urged U.S. District Judge Michael Nachmanoff to dismiss the case, claiming it was driven by vindictiveness. They also raised concerns about Lindsey Halligan, the newly appointed prosecutor who secured the indictment against Comey. The Justice Department's acknowledgment that the full grand jury did not review the final indictment adds to the scrutiny surrounding the prosecution.

Comey was dismissed by President Donald Trump in May 2017 while he was leading an investigation into possible connections between Russia and Trump’s 2016 campaign. Since then, the two have been in a public feud, with Trump labeling Comey as “a weak and untruthful slime ball” and calling for his prosecution.

Earlier this week, another judge involved in the case expressed concerns about “profound investigative missteps,” including potential misstatements of law presented to the grand jury. Halligan initially sought a three-count indictment against Comey, but after one count was rejected, she obtained a two-count indictment accusing him of making a false statement and obstructing Congress. Comey has pleaded not guilty and denies any wrongdoing.

The charges relate to whether Comey authorized an FBI colleague to act as an anonymous source for the media. U.S. Magistrate Judge William Fitzpatrick, who has also reviewed parts of the case, indicated he had doubts about whether the entire grand jury had seen the final indictment. This issue was revisited during Wednesday's hearing, where Nachmanoff pressed the Justice Department on Fitzpatrick’s concerns.

After a private discussion with Halligan, prosecutor Tyler Lemons confirmed that the revised indictment was not presented to all grand jurors. "I was not there, but that is my understanding, your honor," Lemons stated. Halligan later clarified that only two grand jurors, including the foreperson, were present when the final indictment was presented.

Comey’s attorney, Michael Dreeben, argued that the failure to present the final indictment to the entire grand jury warranted dismissal of the case. He also claimed that the statute of limitations for the alleged crimes had expired without a valid indictment. "That would be tantamount to a bar of further prosecution in this case," Dreeben said.

Judge Nachmanoff did not make an immediate ruling, stating that the issues were too complex for a quick decision. Dreeben further contended that the prosecution was vindictive and motivated by Trump’s desire for retribution. He argued, "The president’s use of the Department of Justice to bring a criminal prosecution against a vocal and prominent critic in order to punish and deter those who would speak out against him violates the Constitution."

While motions claiming vindictive prosecution are rarely successful, Dreeben highlighted Trump’s public calls for Comey’s prosecution, including a recent social media post where Trump expressed frustration over the lack of action against his political opponents. "If this is not a direction to prosecute, I’d really be at a loss to say what is," Dreeben remarked.

Trump appointed Halligan, who had no prior prosecutorial experience, as the interim U.S. attorney for the Eastern District of Virginia shortly before she presented the case against Comey. Dreeben suggested that Halligan acted under direction, stating, "She did what she was told to do."

In response, Lemons insisted that Comey was indicted by a "properly constituted" grand jury due to his alleged lawbreaking, not because of any directive from Trump. "The defendant is not being put on trial for anything he said about the president," Lemons asserted. He maintained that Halligan made the decision to prosecute Comey independently.

However, Judge Nachmanoff questioned the timing of Halligan’s appointment, asking, "What independent evaluation could she have done in that time period?" He also inquired about the existence of a "declination memo" that might outline reasons for not pursuing an indictment against Comey, to which Lemons responded that he had been instructed not to disclose that information due to its privileged nature.