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A pair of well-known opponents of former President Trump achieved major court wins on Monday when a federal judge threw out the government's charges filed against them.

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, asserting that the administration and DOJ are simply targeting them for revenge.

US District Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. However, she left the door open for the government to try again.

• Court throws out charges against ex-FBI director Comey and NY attorney general James
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Comey admitted that likelihood after the decision, saying he believes Trump is likely to target him once more.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the last chapter on this matter.

But the DOJ confronts steep obstacles to effectively try either after this defeat, and legal analysts hesitate 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 challenge the ruling?

The Department of Justice can challenge Judge Currie's ruling before a higher appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

US Attorney General Pam Bondi indicated she would take this route, vowing to use all available legal action, including an expedited appeal.

In other cases, the Trump administration has strongly challenged unfavourable rulings, taking cases from lower courts and sometimes accelerating its requests up to the Supreme Court.

Abbe Lowell, an attorney representing James, pledged to keep fighting any further 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 unclear.

Could there be fresh indictments?

The federal prosecutors accused Comey with making false statements to lawmakers and obstruction of justice. Government lawyers charged James with financial fraud and providing false information to a bank.

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

With the original indictments thrown out (although appeals might alter this), the DOJ might try to assemble fresh grand juries and secure new indictments.

As far as everything I've seen, a different attorney could present James's case to a different grand jury and get a new indictment, said Ms Levine.

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

I can tell you it will be hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is able to secure an charge.

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

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

A key issue is the legal time limit – the deadline that government lawyers had to indict him for these particular claims – which expired at the end of September. Nonetheless, the indictment's dismissal would trigger a half-year extension for the DOJ to refile the case.

Still in that case, his lawyers said it intends to argue the prosecution is past the deadline.

The decision further indicates that since the indictment is invalid, the time limit has run and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In both decisions on the indictments against James and Comey, the judge was direct: Halligan's appointment was improper.

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

As a result, Halligan lacked legal power to file the charges, she wrote.

US attorneys are nominated by the US president and require US Senate confirmation. US laws govern how individuals can be appointed on a temporary basis, but the judge determined that Halligan's assignment had violated these laws.

That leaves Halligan's position on subsequent cases against both individuals, once more, unclear.

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

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

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