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A pair of prominent opponents of President Trump secured significant court wins on the start of the week when a US judge threw out the government's charges against them.

Over recent weeks following their charges, former FBI Director James Comey and NY AG Letitia James have argued vehemently that they are innocent, asserting that the administration and DOJ are simply targeting them for retaliation.

Federal Judge Cameron Currie tossed the indictments against them due to prosecutor Lindsey Halligan's improper appointment as federal prosecutor. But she also left open the possibility for the federal authorities to refile the case.

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Comey admitted that likelihood after the ruling, stating he thinks the former president will probably target him again.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the last chapter on this matter.

But the government faces steep obstacles to effectively try either after this setback, and legal analysts hesitate 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 justice department challenge the ruling?

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

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

Previously, the Trump administration has strongly challenged unfavourable rulings, taking cases from lower courts and sometimes fast-tracking its requests up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, vowed to continue to challenge any further politically motivated charges through every lawful means available.

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

Could there be new charges?

The federal prosecutors charged Comey with lying to Congress and obstructing justice. Government lawyers charged James with financial fraud and providing false information to a financial institution.

Both pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, both also asserted to be victims of retaliatory legal action.

With the original indictments thrown out (though, of course, appeals could change that), the government might try to assemble new grand juries and secure new charges.

As far as everything I've seen, a new prosecutor could present James's case to a different grand jury and secure a new indictment, said Ms Levine.

But legal expert 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 strongly disputed, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is able to secure an charge.

He described the complex web of attorneys, judges, and legal filings involved as a legal quagmire with no easy solutions.

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

One problem is the statute of limitations – the deadline that prosecutors had to indict him for these particular claims – which expired at the close of September. Nonetheless, the indictment's dismissal would trigger a six-month grace period for the justice department to refile the case.

Still in that case, his lawyers said it plans to contend the prosecution is out of time.

The ruling also suggests that since the indictment is void, the time limit has run and there can be no further indictment, attorney Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the indictments against James and Comey, the judge was direct: Halligan's appointment was improper.

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

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

US attorneys are nominated by the president and need US Senate confirmation. Federal statutes regulate how people can be assigned on a interim basis, but the judge determined that Halligan's assignment had violated these laws.

That leaves Halligan's position on subsequent cases against James and Comey, once more, unclear.

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

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's appointment was legal, press secretary Karoline Leavitt told reporters on Monday.