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Two prominent opponents of President Trump achieved major legal victories on Monday when a US judge threw out the federal indictments against them.

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have argued fiercely that they are innocent, asserting that the president and justice department are merely targeting them for retaliation.

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

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Comey acknowledged that likelihood after the ruling, stating he believes Trump is likely to target him once more.

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

But the government faces steep hurdles to successfully prosecute both after this defeat, and legal analysts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

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

Could the DOJ challenge the ruling?

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

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

Previously, the Trump administration has aggressively appealed unfavourable rulings, taking cases from lower courts and sometimes accelerating its petitions up to the US Supreme Court.

Abbe Lowell, an attorney representing James, pledged to keep fighting any further politically driven indictments through every lawful means available.

If there is an appeal, the justice department likely would have its own lawyers argue the case, making Halligan's role in the appeals process uncertain.

Is it possible there be new charges?

The federal prosecutors accused Comey with lying to lawmakers and obstructing justice. Federal prosecutors indicted Letitia James with bank fraud and providing false information to a bank.

Both entered not guilty pleas. Besides arguing 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 government might try to assemble new grand juries and obtain new charges.

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

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complex process – 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 appointed and is able to secure an indictment.

He characterized the tangle of lawyers, courts, and motions involved as a procedural morass with no simple answers.

It might be more difficult for the government to try to file the identical accusations against James Comey.

A key issue is the statute of limitations – the deadline that government lawyers had to indict him for these particular claims – which ended at the close of September. However, the dismissal of the charges would trigger a half-year extension for the DOJ to bring the case again.

Still in that situation, his legal team said it plans to argue the prosecution is past the deadline.

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

What is the fate of Lindsey Halligan?

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

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

Therefore, she lacked legal power to file the charges, she wrote.

Federal prosecutors are proposed by the US president and need Senate approval. Federal statutes govern how individuals can be appointed on a interim basis, but Judge Currie found that Halligan's assignment had breached these regulations.

This makes Halligan's position on future 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 serves.

But Bondi said on that day that she made her a special federal prosecutor and praised her work as excellent.

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