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Two prominent opponents of President Trump achieved major court wins on Monday when a federal judge threw out the government's charges filed against them.

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have argued vehemently that they are innocent, claiming that the administration and DOJ are simply targeting them for revenge.

US District Judge Cameron Currie dismissed the indictments in their cases due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. But she also left the door open for the government to try again.

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Comey admitted that likelihood after the ruling, stating he believes the former president is likely to target him again.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the last chapter on this issue.

But the government faces significant obstacles to effectively try either after this setback, and experts are reluctant to forecast what could happen next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, said Professor Kay Levine, Emory University School of Law professor.

Might the DOJ challenge the ruling?

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

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

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

Attorney Abbe Lowell, an attorney representing James, pledged to keep fighting any additional politically motivated charges through every lawful means available.

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

Is it possible there be fresh indictments?

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

Each entered not guilty pleas. Besides claiming Halligan's appointment was invalid, they also asserted to be victims of retaliatory legal action.

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

Based on my analysis, a new prosecutor could bring James' case to a different grand jury and get a new indictment, stated Professor Levine.

But John Day, head 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 hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is can obtain an indictment.

He characterized the tangle of lawyers, judges, and motions involved as a legal quagmire with no easy solutions.

It might be more difficult for the DOJ to try to file the identical accusations against Comey.

One problem is the legal time limit – the time frame that prosecutors had to charge Comey for these particular claims – which expired at the end of September. Nonetheless, the indictment's dismissal would trigger a half-year extension for the justice department to bring the case again.

Even so in that situation, his legal team said it plans to contend the government is out of time.

The ruling also suggests that because the indictment is invalid, the statute of limitations has run and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

In the pair of rulings 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 AG's effort to appoint Ms. Halligan as Interim US Attorney for the Eastern District of Virginia was invalid.

Therefore, she lacked legal power to file the charges, the judge wrote.

Federal prosecutors are nominated by the president and need Senate approval. Federal statutes govern how individuals can be assigned on a interim basis, but the judge determined that Halligan's assignment had breached these regulations.

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

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

But Attorney General Bondi said on Monday that she made Halligan a special federal prosecutor and commended her work as excellent.

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