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Two prominent opponents of former President Trump achieved major legal victories on Monday when a US judge threw out the federal indictments filed against them.

For weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have argued fiercely that they are not guilty, asserting that the administration and DOJ are simply targeting them for revenge.

Federal Judge Cameron Currie tossed the indictments in their cases due to attorney Lindsey Halligan's improper assignment as federal prosecutor. However, she left the door open for the government to refile the case.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
• Federal judge states government 'missteps' may have compromised Comey case
• What is former FBI head James Comey charged with?

Comey admitted that possibility after the decision, saying he believes the former president will probably target him once more.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the final word on this issue.

But the DOJ confronts significant obstacles to successfully prosecute either after this defeat, and experts hesitate to forecast what could occur next due to the unprecedented circumstances of the cases.

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

Might the justice department challenge the ruling?

The DOJ can contest the judge's decision before a federal appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

Previously, the Trump administration has aggressively appealed adverse decisions, taking cases from trial courts and sometimes accelerating its requests up to the US Supreme Court.

Abbe Lowell, James's lawyer, pledged to continue to challenge any additional politically motivated charges through all legal avenues.

If there is 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 new charges?

The federal prosecutors charged James 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. In addition to claiming Halligan was unlawfully appointed, both also asserted to be victims of vindictive prosecution.

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

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 John Day, president of the American College of Trial Lawyers, said it could be a complex process – certainly in the Comey matter.

It's clear that it will be hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is can obtain an indictment.

He described the tangle of attorneys, judges, and legal filings involved as a procedural morass with no easy solutions.

It could be harder for the DOJ to try to file the exact same charges against James Comey.

One problem is the statute of limitations – the time frame that government lawyers had to indict him for these specific allegations – which expired at the close of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the justice department to bring the case again.

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

The ruling also suggests that since the charge is void, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

In both decisions on the charges against Comey and James, the judge was blunt: Halligan was wrongly appointed.

Judge Currie wrote in the James decision that the AG's effort to install Halligan as Interim US Attorney for the Virginia Eastern District was invalid.

Therefore, she lacked legal power to present the indictment, she wrote.

Federal prosecutors are nominated by the president and require US Senate confirmation. Federal statutes regulate how individuals can be appointed on a interim basis, but Judge Currie found that Halligan's appointment had violated these regulations.

This makes Halligan's role on future cases against James and Comey, once more, uncertain.

The decision might also raise doubts on other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

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

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