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

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have argued vehemently 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 against them due to attorney 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 possibility after the ruling, stating he thinks the former president is likely to come after him again.

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

But the DOJ faces significant obstacles to successfully prosecute both 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 uncharted territory, stated Professor Kay Levine, Emory University School of Law professor.

Might the justice department appeal?

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

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

Previously, the former administration has aggressively appealed unfavourable rulings, moving cases from lower courts and sometimes accelerating its petitions up to the US Supreme Court.

Abbe Lowell, James's lawyer, pledged to continue to challenge any additional politically driven indictments through every lawful means available.

In the event of an appeal, the DOJ probably would have its own attorneys present the arguments, making Halligan's involvement in the appeal uncertain.

Could there be new charges?

The government charged Comey with making false statements to lawmakers and obstructing justice. Government lawyers charged James with financial fraud and providing false information to a financial institution.

Both pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, they also asserted to be targets of vindictive prosecution.

Since the initial charges were dismissed (though, of course, appeals could change that), the government might try to convene new grand juries and obtain new charges.

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

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

I can tell you it will be hotly contested, whether Mr Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is able to secure an indictment.

He characterized the tangle of lawyers, courts, and legal filings involved as a legal quagmire with no easy solutions.

It could be harder for the government to try to file the exact same charges against James Comey.

A key issue is the legal time limit – the time frame that government lawyers had to charge Comey for these specific allegations – which expired at the close of September. However, the indictment's dismissal would activate a half-year extension for the DOJ to bring the case again.

Still in that case, his lawyers said it plans to contend the government is out of time.

The decision further indicates that because the indictment is void, the statute of limitations has run and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In both decisions on the indictments against James and Comey, Judge Currie was blunt: Halligan's appointment was improper.

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

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

US attorneys are nominated by the president and require US Senate confirmation. US laws govern how people can be appointed on a interim basis, but the judge determined that Halligan's appointment had violated these regulations.

That leaves Halligan's position on future cases against both individuals, once more, unclear.

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

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

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