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

For weeks following their charges, former FBI Director James Comey and NY AG Letitia James have insisted vehemently that they are innocent, claiming that the president and justice department are merely targeting them for retaliation.

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

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

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

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

But the government faces significant hurdles to effectively try both after this setback, and legal analysts are reluctant to predict what could happen next due to the cases' unprecedented nature.

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

Could the DOJ appeal?

The DOJ can contest 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 indicated she would pursue this option, 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, James's lawyer, pledged to keep fighting any additional politically driven indictments through every lawful means available.

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

Is it possible there be new charges?

The government charged Comey with making false statements to Congress and obstruction of justice. Federal prosecutors indicted Letitia James with bank fraud and making false statements to a bank.

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

Since the initial charges were dismissed (although appeals might alter this), the government might try to convene fresh grand juries and obtain new indictments.

As far as everything I've seen, a new prosecutor could bring James' case to a new grand jury and secure a fresh indictment, stated Professor Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complex process – especially in Comey's case.

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

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

It could be harder for the DOJ to try to bring the identical accusations against Comey.

One problem is the legal time limit – the time frame that government lawyers had to charge Comey for these specific allegations – which expired at the end of September. However, the dismissal of the charges would activate a six-month grace period for the justice department to refile the case.

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

The ruling also suggests that since the indictment is invalid, the time limit has expired and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

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

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

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

Federal prosecutors are proposed by the US president and require Senate approval. Federal statutes govern how people can be assigned on a interim basis, but the judge determined that Halligan's assignment had violated these regulations.

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

The ruling also could cast a shadow on other cases Halligan has prosecuted in the Virginia Eastern District where she works.

But Attorney General Bondi said on that day that she designated her a special federal prosecutor and praised her work as outstanding.

The White House maintained its position that Halligan's appointment was legal, spokesperson Karoline Leavitt told reporters on Monday.