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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 filed against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have argued fiercely that they are not guilty, claiming that the administration and DOJ are merely targeting them for revenge.

US District Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's improper assignment as US attorney. But she also left open the possibility for the federal authorities to try again.

• Court throws out charges against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have tainted the Comey trial
• What are former FBI head James Comey charged with?

Comey admitted that possibility after the ruling, stating he believes 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 last chapter on this matter.

But the government faces steep obstacles to effectively try either after this setback, and legal analysts hesitate to predict what could occur 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 DOJ challenge the ruling?

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

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

In other cases, the Trump administration has strongly challenged adverse decisions, taking cases from trial courts and sometimes fast-tracking its requests up to the Supreme Court.

Attorney Abbe Lowell, James's lawyer, vowed to keep fighting any further politically driven indictments through every lawful means available.

In the event of an appeals process, the DOJ probably would have its own lawyers argue the case, making Halligan's role in the appeal unclear.

Is it possible there be fresh indictments?

The government accused Comey with lying to Congress and obstructing justice. Government lawyers charged James with financial fraud and making false statements to a bank.

Each entered not guilty pleas. Besides arguing Halligan was unlawfully appointed, they also claimed to be targets of retaliatory legal action.

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

As far as everything I've seen, a different attorney could present James's case to a different grand jury and secure a fresh indictment, stated Professor 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 Comey's case can be recharged if a properly assigned attorney is assigned and is can obtain an charge.

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

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

One problem is the statute of limitations – the time frame that prosecutors had to charge him for these specific allegations – which expired at the end of September. However, the dismissal of the charges would activate a six-month grace period 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 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 indictments against James and Comey, the judge was direct: Halligan was wrongly appointed.

Judge Currie wrote in the James decision that the AG's effort to appoint Halligan as Acting US Attorney for the Virginia Eastern District was invalid.

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

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

That leaves Halligan's role on future cases against both individuals, again, unclear.

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

But Bondi said on Monday that she designated Halligan a special US attorney and commended her work as excellent.

The White House maintained its position that Halligan was lawfully appointed, spokesperson Karoline Leavitt told reporters on Monday.