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A pair of high-profile opponents of former President Trump achieved major legal victories on Monday when a federal judge threw out the federal indictments filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have insisted fiercely that they are innocent, asserting that the president and justice department are simply singling out them for revenge.

Federal Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's invalid assignment as federal prosecutor. However, she left the door open for the government to try again.

• Judge dismisses charges against former FBI chief Comey and New York AG James
• Federal judge states government 'missteps' may have compromised Comey case
• What is former FBI head James Comey accused of?

Comey acknowledged that possibility after the ruling, stating he believes the former president is likely to come after him again.

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

But the DOJ faces significant hurdles to effectively try both after this defeat, and legal analysts hesitate to predict what could occur next due to the cases' unprecedented nature.

It feels to me like unexplored legal ground, stated Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

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

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

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

Abbe Lowell, an attorney representing James, pledged to continue to challenge any further politically motivated charges through all legal avenues.

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

Could there be new charges?

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

Each entered not guilty pleas. Besides claiming Halligan's appointment was invalid, they also claimed to be victims of retaliatory legal action.

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

Based on my analysis, a different attorney could bring James' case to a different 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 hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an indictment.

He characterized the complex web of lawyers, judges, and legal filings involved as a procedural morass with no simple answers.

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

A key issue is the legal time limit – the deadline that government lawyers had to indict him for these particular claims – which expired at the end of September. Nonetheless, the indictment's dismissal would trigger a half-year extension for the justice department to bring the case again.

Still in that situation, his lawyers said it intends to contend the prosecution is out of time.

The ruling also suggests that since the charge is void, the time limit has expired and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What is the fate of 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 appoint Ms. Halligan as Acting US Attorney for the Virginia Eastern District was invalid.

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

US attorneys are nominated by the US president and require Senate approval. Federal statutes regulate how individuals can be assigned on a interim basis, but the judge determined that Halligan's appointment had violated these laws.

This makes Halligan's role on subsequent 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 works.

But Bondi said on Monday that she made her a special US attorney and praised her work as excellent.

The White House maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.