By Katelyn Polantz, Kristen Holmes, Holmes Lybrand, Evan Perez, Kara Scannell, CNN

(CNN) — As Lindsey Halligan was driving back to the Washington, DC, area Monday, Trump’s handpicked US attorney to run the Alexandria, Virginia, office was trying to figure out whether she still had a job. Attorney General Pam Bondi called her directly, but offered no clarity, a source familiar with the call told CNN.

Earlier that day, while Halligan was visiting a prosecutors’ office in her district nearly two hours south in Richmond, a federal judge determined she was unlawfully serving in the position. The Justice Department, the judge found, had already used up the 120-day period set aside for interim US attorneys before their nominations by the president must be evaluated by the Senate.

The judge, Cameron McGowan Currie, therefore determined the indictment against former FBI Director James Comey, as well as Halligan’s criminal case against New York Attorney General Letitia James, were invalid.

Another judge had days before slammed Halligan’s lawyering before the grand jury in the Comey case as so problematic, it raised questions about whether the case could continue.

The dismissal of Comey’s case led to a scramble among the Justice Department prosecutors in the office she led, in a dramatic and polarizing fashion, for nine weeks. The prosecutors now didn’t know whether they should still list Halligan as their supervisor on court filings. Halligan herself was unclear and waiting on directives from Justice Department headquarters, a source told CNN.

Even now, days later, Halligan’s future as a top prosecutor remains in a sort of purgatory — with Justice Department officials still working through how they might bring the cases against Comey and James back to life — and her position inside the US attorney’s office up for debate. A source familiar with Halligan says she has been excluded from these ongoing conversations.

Another official close to Justice Department headquarters, however, disputed that Halligan wasn’t part of those conversations, and said any confusion was coming from within the local prosecutors’ office. The official said senior DOJ leadership has had discussions with Halligan before and after McGowan Currie’s ruling.

The official familiar with the matter said the DOJ prepared guidance to be sent to everyone in the Alexandria office that said Halligan wasn’t removed as a result of McGowan Currie’s ruling.

The events of Halligan’s 63 days as interim US attorney empowered by President Donald Trump himself, her former private client, have eroded the bench of experienced prosecutors in the once-premier Alexandria-based prosecutors’ office. Many fear the court itself will look differently at the credibility of Justice Department attorneys.

“There’s less trust in the office, generally speaking,” one person familiar with the office’s prosecutors told CNN recently.

From White House adviser to Trump’s most important prosecutor

Days before a five-year window closed on September 30 for Comey to face charges over congressional testimony in 2020, then-US Attorney Erik Siebert was pushed out of the position. Siebert had hesitated on bringing the cases against Comey and James, after career prosecutors in the US attorney’s office pushed back against the viability of doing so.

Shortly after Siebert’s ouster, Trump posted a stunning public message addressed to “Pam” on his Truth Social account. In it, he told Bondi they couldn’t “delay any longer” when it came to bringing charges against his political enemies — specifically citing Sen. Adam Schiff, Comey and James. Trump also suggested that Halligan, a White House adviser who was currently working on reviewing exhibits in Smithsonian museums, take over the Virginia office and the cases he wanted to see prosecuted.

“Lindsey Halligan is a really good lawyer, and likes you, a lot,” Trump wrote. Later, he posted that he intended to nominate Halligan, a former insurance lawyer, to the post.

Halligan had previously only ever been a lawyer on cases in federal court for a few of Trump’s civil matters, and had no prosecutorial experience.

But she had the confidence and the drive to deliver for the president.

A source close to Halligan told CNN that despite being the Trump administration’s selection, Justice Department headquarters declined to provide lawyers to assist Halligan as she prepared to appear before a grand jury in Alexandria with evidence against Comey, and at least one other prosecutor in the Eastern District of Virginia declined to accompany her. FBI agents and lawyers working to prepare her on the case were denied a paralegal to assist in the presentation to the grand jury, multiple sources told CNN. Top Justice Department officials told the White House they had offered to help.

Halligan then began a crash course to prepare, spending hours with FBI attorneys and agents who led the investigation.

But Justice Department officials told her that the deputy attorney general’s office — led by Trump’s former personal attorney Todd Blanche — didn’t have lawyers to help her, and that it was against federal rules of criminal procedure for an attorney from DOJ headquarters to be in the grand jury room when she presented Comey’s case.

“Baseless palace intrigue stories like this won’t distract or deter this Department of Justice from our mission to make America safe again,” the Justice Department said in a statement to CNN.

“The outstanding team of US Attorneys assembled by Attorney General Bondi and Deputy Attorney General Blanche are fully empowered and supported to uphold the rule of law, prosecute crime, and protect our communities—and especially in light of this week’s horrific attack against the National Guard, this Department will remain focused on its mission to take America back from those who hate our values and endanger our citizens,” the statement continued.

Internal office fallout

Trump’s installment of Halligan immediately prompted distrust and disappointment among the career prosecutors working in the Eastern District of Virginia.

The prosecutors based in Alexandria carried out some of the Justice Department’s most high-profile and sensitive investigations, especially related to national security. And Trump’s wish to rout out prosecutors he didn’t trust had largely not affected that district.

“It was viewed as a relatively stable and safe place to be. People were able to put their heads down and work,” one person familiar with the office told CNN.

Within two weeks of Halligan’s landing, however, the district’s top national security prosecutor, Michael Ben’Ary, and others were fired with little reason given, and they began hitting back at her and other Trump administration officials’ decisions. Comey’s son-in-law, who was a deputy national security chief in the Alexandria office, also resigned on the evening of Comey’s indictment.

Ben’Ary taped a note on his former office door as he exited, writing to “my EDVA colleagues” that “the decisions to remove experienced career officials from US Attorneys Offices, the FBI, and other critical parts of DOJ undermines our country’s ability to counter terrorist organizations, malign nation-state actors, and countless others that seek to harm our nation and its citizens.”

Ben’Ary’s departure came in the middle of the office’s criminal prosecution of an alleged terrorist for the 2021 bombing of a civilian gate at the international airport in Kabul, Afghanistan. The case is still headed to trial, and the defendant’s lawyers have asked a judge to formally disqualify Halligan from directing the prosecution.

After Halligan indicted Letitia James on mortgage fraud charges, more heads began to roll. Elizabeth Yusi, who wrote an internal memo outlining why prosecutors didn’t believe there was enough evidence to support charges against James, and Kristin Bird, her deputy, were fired. News of the memo was publicly reported. A source close to Halligan said Yusi never voiced concerns about the case to Halligan. The source said Halligan was not made aware of the memo.

Halligan believed attorneys were leaking information about separate investigations to the media, CNN previously reported.

Another prosecutor, Maggie Cleary, a well-connected Republican who had landed in the office shortly before as Halligan’s No. 2, was sidelined and moved out to a role in the department’s Washington headquarters.

Paranoia began to grow inside the once stable office. Shortly after Ben’Ary’s departure, prosecutors started to believe that Halligan was working closely with Ed Martin, the Trump administration’s pardon attorney who also pushed for prosecutions of the president’s political enemies — especially James — and the exoneration of MAGA allies.

Martin visited the Alexandria US attorney’s office during Halligan’s tenure, sources told CNN, adding to the speculation. One source told CNN he was delivering binders on James’ properties at that time and was never involved in daily decisions.

Nonetheless, Eastern District of Virginia prosecutors grew concerned Halligan might install Martin as her second-in-command, which was a career position, the sources told CNN. A source familiar with the dynamic said Halligan was never considering this option.

Though Halligan had gotten the public political boosts of securing the Comey and James indictments, inside the office she was largely absent from interacting with the career prosecutors who staffed many of the cases. Halligan attended meetings with the team fairly regularly, but she did not build close relationships.

The distance between Halligan and the career attorneys isn’t just in terms of communication, one person said. Halligan has been seen walking with court security by her side even inside the office.

Some were told by security in the Alexandria building that Halligan may have placed cameras around the office to more closely monitor her workforce.

The security cameras may have been a planned project, but people familiar with the office described them as among the changes that added “paranoia” to the environment.

Halligan disputed the allegations.

“The allegation that I installed, directed the installation of, or had any involvement with installing security-camera equipment in the office is completely false,” Halligan said in a statement to CNN. “Any review, audit or questioning of those in charge of the security systems will confirm that I had no role - direct or indirect - in their installation or operation.”

Grand jury tumult

The choice to have Halligan solely present two of Trump’s most sought-after indictments to grand jurors has been heavily scrutinized.

Two judges in the Eastern District of Virginia trial-level federal court have read the grand jury transcripts, and questioned what Halligan said to the grand jurors.

“The court has identified two statements by the prosecutor to the grand jurors that on their face appear to be fundamental misstatements of the law that could compromise the integrity of the grand jury process,” Judge William Fitzpatrick wrote in an opinion on November 17. The judge said that after Halligan told the grand jurors she was their legal adviser, she appeared to suggest Comey would need to testify at his trial and that the Justice Department may have more and better evidence later.

Halligan’s exact words are redacted in public court records. The Justice Department has disputed Fitzpatrick’s read of the situation.

The judges have also questioned how she skipped presenting the final indictment in the full secret proceeding, after grand jurors only agreed to approve only two-thirds of the Comey charges.

Issues of how Halligan presented the case came to a head during a hearing earlier this month when she told a judge the full grand jury had not reviewed the final indictment she signed against Comey.

At a court hearing on November 19, the lead attorney for the Justice Department, Tyler Lemons, whom Halligan had brought in from North Carolina to handle the Comey case, told the judge only one indictment was presented to the grand jury. The grand jurors told the court in a filing that they hadn’t approved it, then later that original filing was marked to say the grand jury approved two of three charges Halligan presented.

After going briefly silent, then needing to confirm what he heard, Judge Michael Nachmanoff turned to Halligan.

“Ms. Halligan, you can come to the podium. You’re counsel of record. You can address the court. It might be easier,” the judge said.

She attempted to cut the judge off before he finished speaking, to tell him his impression was wrong.

She explained in court that a foreperson and another grand juror were present when they handed up the indictment. She said that the foreperson said in open court that day that they were declining to indict on the first charge on the document, but were indicting on the second and third charges — making a false statement to Congress and obstructing a congressional proceeding. Halligan’s explanation confirmed that what the judge called the “operative” indictment against Comey wasn’t formally presented to the full grand jury.

“I’m familiar with the transcript,” the judge said, then told her to sit down.

“OK,” Halligan responded.

Halligan’s grand jury work also raised questions in the case against James, the New York attorney general. But those issues hadn’t been fully fleshed out in court before a judge dismissed her case on November 24.

Other prosecutors previously working with a grand jury in Norfolk — another courthouse in the Eastern District of Virginia — hadn’t moved to indict the case, even after Trump posted on social media pushing Bondi to charge James, Comey and another political adversary, Democratic Sen. Schiff.

Halligan there, too, presented the James mortgage fraud indictment to a grand jury in Alexandria over one afternoon in early October. Halligan had gone through the case with the FBI — and asked for all possible evidence. She determined that while two of James’ properties were under investigation, there was only one probe investigation with enough evidence to take to the grand jury. With schedule changes, Halligan avoided the four-hour drive to Norfolk and brought the charges before a grand jury in Alexandria, once again, by herself.

Halligan secured an indictment against James that afternoon. While she had told department headquarters she would bring the case against James, she did not brief them that she had decided to bring it that day. Top officials learned Halligan had secured the indictment from news reports.

What’s next for Halligan

Justice Department officials are still working through how they might bring the cases against Comey and James back to life.

The cumulative effect on Halligan’s reputation, despite Bondi calling her an “excellent US attorney” last week, has been severe.

In just two months, Halligan went from being the primary prosecutor going after the president’s political enemies, to a headache for the Justice Department who installed her — with prosecutors unclear how to proceed with the two cases and others presented under her authority.

Her name remains on court filings. As of Wednesday afternoon, prosecutors in the office were instructed to add Blanche, the deputy attorney general, and the office’s new first assistant, Robert McBride, on the court documents.

In the third email in 48 hours on what the office’s signature block used in court should say, Justice Department officials instructed the US attorney’s office to keep Halligan listed, now as both “Unites States Attorny” — which was misspelled in the internal email — and as a “special” United States Attorney, according to a copy reviewed by CNN.

Halligan is still waiting for directives from Justice Department headquarters. To some, it was unclear as of Friday whether she would show up at the office in Alexandria on Monday.

The Justice Department still hasn’t taken the next steps in the cases against Comey and James, which the judge said may have the ability to be charged again. No appeal has been filed in either to contest the judge’s ruling that Halligan was not a valid prosecutor in September and October, despite Justice Department leadership and the White House announcing that as the plan.

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