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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.

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

Federal Judge Cameron Currie tossed the indictments against them due to prosecutor Lindsey Halligan's invalid assignment as US attorney. However, she left the door open for the federal authorities to try again.

• Court throws out charges against ex-FBI director Comey and New York AG James
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Comey admitted that likelihood after the decision, stating he thinks the former president is likely to target him again.

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

But the DOJ faces significant hurdles to successfully prosecute either after this defeat, and legal analysts are reluctant to forecast what could happen next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, said Kay Levine, Emory University School of Law professor.

Could the justice department appeal?

The Department of Justice can challenge 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 pursue this option, vowing to use all available legal action, including an immediate appeal.

In other cases, the Trump administration has aggressively appealed unfavourable rulings, moving cases from trial courts and sometimes accelerating its requests up to the Supreme Court.

Abbe Lowell, an attorney representing James, vowed to continue to challenge any further politically driven indictments through all legal avenues.

In the event of an appeals process, the justice department probably would have its own lawyers present the arguments, making Halligan's involvement in the appeals process unclear.

Could there be new charges?

The federal prosecutors charged James Comey with lying to lawmakers and obstruction of justice. Federal prosecutors charged James with bank fraud and providing false information to a bank.

Each entered not guilty pleas. Besides claiming Halligan's appointment was invalid, both also asserted to be targets of retaliatory legal action.

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

Based on my analysis, a new prosecutor could present James's case to a different grand jury and get a new indictment, said Ms 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 strongly disputed, whether Comey's case can be recharged if a properly assigned attorney is assigned and is able to secure an indictment.

He characterized the tangle of lawyers, courts, and legal filings involved as a legal quagmire with no simple answers.

It might be more difficult for the DOJ to try to bring the exact same charges against Comey.

One problem is the legal time limit – the deadline that prosecutors had to charge Comey for these specific allegations – which expired at the close of September. However, the dismissal of the charges would trigger a six-month grace period for the justice department to bring the case again.

Even so in that case, his legal team said it intends to argue the government is out of time.

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

What happens to Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

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

As a result, she had no lawful authority to present the indictment, the judge wrote.

US attorneys are proposed by the US president and require US Senate confirmation. Federal statutes govern how people can be assigned on a temporary basis, but the judge determined that Halligan's appointment had breached these regulations.

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

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

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

The administration stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.