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Two well-known opponents of President Trump obtained significant court wins on the start of the week when a federal judge threw out the federal indictments against them.

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

Federal Judge Cameron Currie dismissed the charges in their cases due to prosecutor Lindsey Halligan's invalid assignment as US attorney. However, she left open the possibility for the government to refile the case.

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Comey admitted that possibility after the decision, stating he believes the former president will probably target him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the last chapter on this matter.

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

It feels to me like unexplored legal ground, stated Kay Levine, law professor at Emory University.

Could the justice department appeal?

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

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

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

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any additional politically driven indictments through every lawful means available.

If there is an appeal, the DOJ probably would have its own attorneys argue the case, making Halligan's involvement in the appeal unclear.

Is it possible there be fresh indictments?

The federal prosecutors accused Comey with making false statements to Congress and obstruction of justice. Government lawyers indicted James with bank fraud and making false statements to a financial institution.

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

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

Based on my analysis, a new prosecutor could bring James' case to a different grand jury and get a fresh indictment, stated Ms Levine.

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

I can tell you it will be hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is can obtain an charge.

He characterized the tangle of lawyers, judges, and legal filings involved as a procedural morass with no easy solutions.

It might be harder for the DOJ to try to file the exact same charges against James Comey.

A key issue is the statute of limitations – the deadline that prosecutors had to charge Comey for these specific allegations – which ended at the close of September. Nonetheless, the indictment's dismissal would trigger a half-year extension for the justice department to bring the case again.

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

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

The judge stated in the James ruling that the Attorney General's attempt 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.

US attorneys are proposed by the president and need US Senate confirmation. US laws regulate how individuals can be assigned on a temporary basis, but the judge determined that Halligan's appointment had violated these laws.

This makes Halligan's role on future cases against both individuals, again, unclear.

The ruling also could cast a shadow on other cases Halligan has brought in the Eastern District of Virginia where she serves.

But Bondi said on that day that she designated Halligan a special US attorney and praised her work as outstanding.

The White House stood by its stance that Halligan's appointment was legal, press secretary Karoline Leavitt told the press on Monday.