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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 since their indictments, ex-FBI chief James Comey and NY AG Letitia James have argued fiercely that they are not guilty, claiming that the administration and DOJ are simply targeting them for revenge.

US District Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. However, she left the door open for the government to try again.

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

And White House spokesperson Abigail Jackson appeared to agree: This will not be the last chapter on this matter.

But the government confronts steep hurdles to successfully prosecute both after this setback, and legal analysts hesitate to forecast what could happen next due to the cases' unprecedented nature.

It feels to me like uncharted territory, said Kay Levine, Emory University School of Law professor.

Might the DOJ appeal?

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

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

In other cases, the Trump administration has aggressively appealed unfavourable rulings, taking cases from lower courts and sometimes fast-tracking its requests up to the US Supreme Court.

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

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

Could there be new charges?

The government charged Comey with lying to Congress and obstructing justice. Federal prosecutors indicted Letitia James with bank fraud and providing false information to a financial institution.

Each entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, they also claimed to be targets 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 secure new indictments.

Based on my analysis, a different attorney could bring James' case to a new grand jury and secure a fresh indictment, said Professor Levine.

But 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 strongly disputed, whether Mr Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is able to secure an indictment.

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

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 time frame that government lawyers had to indict him for these particular claims – which expired at the close of September. However, the indictment's dismissal would trigger a six-month grace period for the justice department to refile the case.

Even so in that situation, his legal team said it intends to argue the prosecution is out of time.

The ruling also suggests that because the charge is invalid, the statute of limitations has expired and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

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

Judge Currie wrote in the James decision that the Attorney General's attempt to appoint Ms. Halligan as Interim US Attorney for the Eastern District of Virginia was invalid.

Therefore, Halligan had no lawful authority to present the indictment, she wrote.

Federal prosecutors are nominated by the US president and need US Senate confirmation. US laws govern how people can be assigned on a temporary basis, but Judge Currie found that Halligan's assignment had breached these laws.

This makes Halligan's position on subsequent cases against James and Comey, once more, uncertain.

The ruling also could cast a shadow on other cases Halligan has brought 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 outstanding.

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