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A pair of well-known opponents of President Trump achieved significant court wins on Monday when a US judge threw out the government's charges filed against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have insisted vehemently that they are innocent, claiming that the administration and DOJ are merely targeting them for retaliation.

Federal Judge Cameron Currie dismissed the charges against them due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. However, she left open the possibility for the federal authorities to try again.

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Comey admitted that possibility after the ruling, saying he believes the former president will probably target him again.

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

But the DOJ confronts significant obstacles to successfully prosecute both after this setback, and experts hesitate to predict what could happen next due to the cases' unprecedented nature.

In my view, it's uncharted territory, stated Kay Levine, law professor at Emory University.

Could the justice department appeal?

The Department of Justice can contest Judge Currie's ruling before a higher appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

US Attorney General Pam Bondi indicated she would pursue this option, vowing to use all available legal action, including an immediate appeal.

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

Attorney Abbe Lowell, an attorney representing James, pledged to continue to challenge any further politically driven indictments through every lawful means available.

If there is an appeal, the justice department probably would have its own attorneys argue the case, making Halligan's role in the appeals process uncertain.

Could there be fresh indictments?

The government accused Comey with making false statements to Congress and obstruction of justice. Government lawyers charged James with financial fraud and making false statements to a financial institution.

Both pleaded not guilty. Besides arguing Halligan was unlawfully appointed, they also claimed to be victims of retaliatory legal action.

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

As far as everything I've seen, a different attorney could present James's 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 complex process – especially in the Comey matter.

I can tell you it will be hotly contested, whether Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is can obtain an charge.

He described the tangle of lawyers, courts, and motions involved as a procedural morass with no easy solutions.

It might be more difficult for the government to try to file the exact same charges against James Comey.

One problem is the statute of limitations – the deadline that government lawyers had to charge Comey for these particular claims – which ended at the close of September. However, the dismissal of the charges would activate a half-year extension for the justice department to refile the case.

Still in that case, his legal team said it plans to argue the government is out of time.

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

What is the fate of Lindsey Halligan?

In both decisions on the charges against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

Judge Currie wrote in the James ruling that the Attorney General's attempt to appoint Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

As a result, she lacked legal power to present the indictment, she wrote.

Federal prosecutors are nominated by the US president and need Senate approval. US laws regulate how individuals can be appointed on a interim basis, but the judge determined that Halligan's appointment had violated these regulations.

This makes Halligan's role on subsequent cases against James and Comey, again, uncertain.

The decision might also cast a shadow on other cases Halligan has prosecuted in the Eastern District of Virginia where she serves.

But Attorney General Bondi said on that day that she made Halligan a special US attorney and praised her work as outstanding.

The administration stood by its stance that Halligan's appointment was legal, press secretary Karoline Leavitt told reporters on Monday.