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Two prominent opponents of President Trump achieved major legal victories on the start of the week when a US judge dismissed the government's charges filed against them.

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are innocent, claiming that the administration and DOJ are simply singling out them for revenge.

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

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Comey acknowledged that likelihood after the decision, stating he believes Trump is likely to target him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the final word on this issue.

But the DOJ faces steep obstacles to effectively try either after this setback, and experts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

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

Could the justice department challenge the ruling?

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

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

In other cases, the Trump administration has strongly challenged adverse decisions, moving cases from trial courts and sometimes fast-tracking its requests up to the Supreme Court.

Abbe Lowell, an attorney representing James, vowed to keep fighting any additional politically motivated charges through all legal avenues.

If there is an appeals process, the justice department likely would have its own lawyers present the arguments, making Halligan's involvement in the appeals process unclear.

Could there be fresh indictments?

The government accused Comey with lying to lawmakers and obstructing justice. Government lawyers indicted James with bank fraud and providing false information to a bank.

Both entered not guilty pleas. Besides arguing Halligan was unlawfully appointed, both also claimed to be targets of vindictive prosecution.

Since the initial charges were dismissed (although appeals might alter this), the DOJ might try to convene fresh grand juries and obtain new charges.

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

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

It's clear that it will be hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an charge.

He described the tangle of attorneys, judges, and motions involved as a legal quagmire with no easy solutions.

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

One problem is the legal time limit – the deadline that prosecutors had to indict Comey 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.

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

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

What is the fate of prosecutor Lindsey Halligan?

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

Judge Currie wrote in the James ruling that the AG's effort to appoint Halligan as Interim US Attorney for the Eastern District of Virginia was unlawful.

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

Federal prosecutors are nominated by the president and need US Senate confirmation. Federal statutes regulate how individuals can be appointed on a temporary basis, but the judge determined that Halligan's appointment had breached these regulations.

This makes Halligan's position on future cases against both individuals, again, uncertain.

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

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

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