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A pair of high-profile critics of President Trump secured significant legal victories on Monday when a federal judge threw out the government's charges filed against them.

For weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have argued vehemently that they are not guilty, asserting that the president and justice department are merely singling out them for retaliation.

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. But she also left the door open for the federal authorities to try again.

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Comey admitted that likelihood after the ruling, saying he thinks the former president is likely to come after him again.

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

But the DOJ faces significant obstacles to successfully prosecute either after this setback, and legal analysts hesitate to predict what could happen next due to the cases' unprecedented nature.

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

Could the justice department appeal?

The DOJ can contest Judge Currie's ruling before a federal appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

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

In other cases, the former administration has aggressively appealed adverse decisions, moving cases from lower courts and sometimes fast-tracking its requests up to the Supreme Court.

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

In the event of an appeals process, the DOJ likely would have its own lawyers present the arguments, making Halligan's role in the appeals process uncertain.

Could there be fresh indictments?

The federal prosecutors charged Comey with making false statements to Congress and obstruction of justice. Federal prosecutors charged James with financial fraud and making false statements to a bank.

Both entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, both also asserted to be targets of retaliatory legal action.

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to convene new grand juries and obtain new indictments.

Based on my analysis, a new prosecutor could bring James' case to a new grand jury and secure a new indictment, said Ms Levine.

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

It's clear that it will be strongly disputed, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is able to secure an charge.

He described the complex web of lawyers, courts, and legal filings involved as a legal quagmire with no simple answers.

It might be more difficult for the government to try to file the exact same charges against Comey.

A key issue is the statute of limitations – the time frame that prosecutors had to charge Comey for these specific allegations – which ended at the close of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the DOJ to bring the case again.

Still in that case, his lawyers 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 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 was wrongly appointed.

The judge stated in the James decision that the AG's effort to appoint Halligan as Acting US Attorney for the Eastern District of Virginia was invalid.

Therefore, she had no lawful authority to file the charges, she wrote.

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

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

The ruling also could raise doubts on other cases Halligan has brought in the Virginia Eastern District where she serves.

But Bondi said on that day that she made her a special US attorney and commended her work as outstanding.

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