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Two well-known opponents of President Trump obtained major court wins on the start of the week when a federal judge threw out the federal indictments against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have insisted fiercely that they are not guilty, asserting that the administration and DOJ are merely targeting them for revenge.

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's invalid assignment as US attorney. But she also left the door open for the federal authorities to refile the case.

• Judge dismisses cases against former FBI chief Comey and NY attorney general James
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Comey admitted that likelihood after the decision, saying he thinks Trump will probably target him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the last chapter on this issue.

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

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 case, that would be the Fourth Circuit Court of Appeals.

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

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

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

If there is an appeal, the justice department probably would have its own lawyers present the arguments, making Halligan's role in the appeal unclear.

Is it possible there be fresh indictments?

The federal prosecutors accused Comey with making false statements to Congress and obstructing justice. Government lawyers indicted James with bank fraud and providing false information to a financial institution.

Each pleaded not guilty. In addition to claiming Halligan's appointment was invalid, they also claimed to be victims of vindictive prosecution.

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

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

But John Day, head of the American College of Trial Lawyers, said it could be a complicated path – certainly in the Comey matter.

I can tell you it will be strongly disputed, whether Comey's case can be re-indicted if a properly assigned attorney is appointed and is able to secure an indictment.

He characterized the complex web of attorneys, judges, and motions involved as a procedural morass with no simple answers.

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

A key issue is the legal time limit – the time frame that government lawyers had to charge him for these specific allegations – which ended at the close of September. Nonetheless, the dismissal of the charges would trigger a six-month grace period for the DOJ to refile the case.

Even so in that case, his lawyers said it plans to argue the government is past the deadline.

The decision further indicates that since the charge is invalid, the statute of limitations has expired and there can be no further indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

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

The judge stated in the James ruling that the AG's effort to install Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

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

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

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

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

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

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