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Two prominent critics of President Trump obtained major court wins on the start of the week when a federal judge dismissed the government's charges filed against them.

For weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained fiercely that they are not guilty, claiming that the administration and DOJ are simply singling out them for retaliation.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. However, she left the door open for the government to refile the case.

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Comey acknowledged that possibility after the ruling, stating he believes the former president will probably target him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the final word on this matter.

But the DOJ faces steep hurdles to successfully prosecute both after this defeat, and experts hesitate to forecast what could happen next due to the cases' unprecedented nature.

It feels to me like uncharted territory, said Professor Kay Levine, law professor at Emory University.

Could the justice department challenge the ruling?

The Department of Justice can challenge the judge's decision before a federal appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

Attorney General Pam Bondi signaled she would take this route, vowing to use all available legal action, including an immediate appeal.

Previously, the Trump administration has strongly challenged adverse decisions, moving cases from lower courts and sometimes fast-tracking its petitions up to the Supreme Court.

Abbe Lowell, an attorney representing James, pledged to continue to challenge any additional politically motivated charges through all legal avenues.

In the event of an appeal, the justice department likely would have its own attorneys present the arguments, making Halligan's role in the appeals process uncertain.

Could there be fresh indictments?

The federal prosecutors charged Comey with making false statements to Congress and obstruction of justice. Government lawyers charged Letitia James with bank fraud and making false statements to a financial institution.

Both entered not guilty pleas. In addition to claiming Halligan was unlawfully appointed, they also asserted to be victims of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the DOJ might try to convene new grand juries and obtain new charges.

Based on my analysis, a different attorney could bring James' case to a different grand jury and get a fresh indictment, said Professor Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly in Comey's case.

I can tell you it will be strongly disputed, whether Comey's case can be recharged if a properly assigned attorney is appointed and is can obtain an indictment.

He described the tangle of lawyers, judges, and legal filings involved as a legal quagmire with no simple answers.

It could be harder for the government to try to bring the exact same charges against James Comey.

One problem is the legal time limit – the time frame that government lawyers had to charge him for these particular claims – which ended at the end of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the DOJ to refile the case.

Even so in that case, his legal team said it plans to argue the prosecution is out of time.

The decision further indicates that since the charge is void, the time limit has expired and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

In both decisions on the charges against James and Comey, Judge Currie was blunt: Halligan's appointment was improper.

The judge stated in the James decision that the Attorney General's attempt to appoint Halligan as Interim US Attorney for the Eastern District of Virginia was invalid.

Therefore, Halligan had no lawful authority to file the charges, the judge wrote.

Federal prosecutors are proposed by the president and need US Senate confirmation. Federal statutes govern how people can be appointed on a interim basis, but Judge Currie found that Halligan's assignment had breached these laws.

That leaves Halligan's role on future cases against both individuals, again, uncertain.

The ruling also could raise doubts on other cases Halligan has prosecuted in the Eastern District of Virginia where she serves.

But Bondi said on Monday that she designated her a special US attorney and commended her work as outstanding.

The White House maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.