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Two prominent opponents of President Trump obtained significant court wins on Monday when a federal judge threw out the federal indictments filed against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have argued fiercely that they are not guilty, asserting that the administration and DOJ are simply singling out them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's invalid assignment as US attorney. But she also left open the possibility for the government to try again.

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Comey acknowledged that possibility after the ruling, saying he thinks Trump is likely to target him again.

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

But the government faces steep obstacles to successfully prosecute either after this setback, and experts hesitate to forecast what could occur next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, stated Professor Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

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

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

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

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any additional politically motivated charges through all legal avenues.

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

Is it possible there be fresh indictments?

The government accused Comey with making false statements to lawmakers and obstruction of justice. Federal prosecutors indicted James with bank fraud and making false statements to a bank.

Both entered not guilty pleas. In addition to claiming Halligan was unlawfully appointed, both also asserted to be victims of vindictive prosecution.

Since the initial charges were dismissed (although appeals might alter this), the government might try to convene new grand juries and secure new indictments.

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

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complex process – certainly in Comey's case.

It's clear that 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 charge.

He characterized the complex web of attorneys, judges, and legal filings involved as a procedural morass with no easy solutions.

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

One problem is the statute of limitations – the deadline that prosecutors had to indict Comey for these specific allegations – which expired at the end of September. However, the indictment's dismissal would trigger a six-month grace period for the DOJ to bring the case again.

Even so in that case, his lawyers said it plans to contend the prosecution is out of time.

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

What happens to 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 Attorney General's attempt to install Halligan as Interim US Attorney for the Eastern District of Virginia was invalid.

Therefore, she lacked legal power to present the indictment, the judge wrote.

Federal prosecutors are nominated by the president and need Senate approval. Federal statutes govern how people can be assigned on a interim basis, but Judge Currie found that Halligan's appointment had violated these regulations.

That leaves Halligan's role on future cases against both individuals, once more, uncertain.

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

But Bondi said on Monday that she made Halligan a special US attorney and praised her work as excellent.

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