FILE PHOTO: Lawyers for former U.S. President Donald Trump; James Trusty, Lindsey Halligan and John Rowley, depart the U.S. Justice Department after meeting with Justice Department officials over the Trump Mar-a-Lago classified documents case, after Trump's lawyers last month sent the department a letter asking for a meeting with U.S. Attorney General Merrick Garland, in Washington, U.S. June 5, 2023. REUTERS/Sarah Lynch/File Photo

U.S. Attorney Lindsey Halligan appeared in court on Wednesday as former FBI Director James Comey challenged his indictment in an Alexandria, Virginia, courtroom. Among the challenges for the Justice Department was a judge demanding answers as prosecutors insisted they weren't trying to be evasive.

Comey is citing years of evidence from Trump's own social media to challenge the "vindictive" or "selective" prosecution.

“The President’s hate or animosity or dislike of Mr. Comey may be enough to fire" him, Comey defense lawyer Michael Dreeben told U.S. District Judge Michael Nachmanoff. But the lawyer argued it can't be used to throw the “full weight" of the criminal justice system against him.

Dreeben pointed to Trump's Truth Social post from late September in which Trump appeared to send a message to Attorney General Pam Bondi and championed the appointment of Halligan in former U.S. Attorney Erik Siebert's place.

“The President is underscoring what he wants here, Siebert was not doing his job here," Dreeben said.

“If that’s not a direction to prosecute, I’m not really sure what is,” he added.

Prosecutor Tyler Lemons later argued Comey wasn't "indicted at the direction of the president of the United States."

Lemons said the grand jury's work on the indictment was entirely proper.

“We’ll have some questions about that,” Judge Michael Nachmanoff said.

As CNN captured, the judge began demanding answers about a rumored memo that says they didn't have the evidence to indict Comey.

“What did someone in the Deputy Attorney General’s office instruct you not to say?” Judge Nachmanoff asked.

Lemons confessed that he has “reviewed” draft memorandums.

He then promised, “I hope you understand that I am trying to answer your questions."

U.S. Magistrate Judge William Fitzpatrick in the Eastern District of Virginia on Monday chastised Halligan after reviewing the grand jury transcripts. He wrote that he found a "disturbing pattern of profound investigative missteps" by the Department of Justice, and warned it imperils her case against Comey.

One CNN reporter said Tuesday that there are so many flaws cited by Fitzpatrick that the case may not even make it to trial.