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Two well-known opponents of President Trump achieved significant legal victories on Monday when a US judge threw out the government's charges filed against them.

For weeks following their charges, former FBI Director James Comey and NY AG Letitia James have maintained fiercely that they are innocent, asserting that the administration and DOJ are merely targeting them for revenge.

Federal Judge Cameron Currie dismissed the charges against them due to prosecutor Lindsey Halligan's invalid appointment as US attorney. However, she left open the possibility 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 the Comey trial
• What are former FBI head James Comey accused of?

Comey acknowledged that possibility after the ruling, saying he thinks the former president will probably come after him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the last chapter on this matter.

But the DOJ confronts steep hurdles to effectively try both after this defeat, and experts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, said Professor Kay Levine, Emory University School of Law professor.

Could the DOJ appeal?

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

US Attorney General Pam Bondi signaled she would take this route, pledging to use all legal means, including an expedited appeal.

In other cases, the former administration has strongly challenged adverse decisions, taking cases from trial courts and sometimes accelerating its requests up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to keep fighting any additional politically motivated charges through all legal avenues.

In the event of an appeal, the DOJ probably would have its own attorneys present the arguments, making Halligan's involvement in the appeal uncertain.

Is it possible there be new charges?

The government accused Comey with lying to lawmakers and obstructing justice. Federal prosecutors charged Letitia James with financial fraud and providing false information to a financial institution.

Each pleaded not guilty. Besides claiming Halligan was unlawfully appointed, they also asserted to be victims of retaliatory legal action.

Since the initial charges were dismissed (though, of course, appeals could change that), the government might try to convene fresh grand juries and obtain new charges.

Based on my analysis, a different attorney could present James's case to a new grand jury and get a new indictment, said Professor Levine.

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complicated path – especially in the Comey matter.

I can tell you it will be hotly contested, whether Mr Comey's case can be recharged if a properly assigned attorney is assigned and is can obtain an charge.

He described the complex web of attorneys, courts, and motions involved as a legal quagmire with no simple answers.

It might be harder for the government to try to bring the exact same charges against James Comey.

A key issue is the statute of limitations – the deadline that government lawyers had to indict him for these specific allegations – which ended at the end of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the justice department to refile the case.

Still in that situation, his lawyers said it plans to argue the government is past the deadline.

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

What happens to prosecutor Lindsey Halligan?

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

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

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

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

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

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

But Bondi said on that day that she designated her a special US attorney and praised her work as excellent.

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