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Two prominent opponents of former President Trump achieved major court wins on Monday when a federal judge dismissed the government's charges against them.

Over recent weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have maintained fiercely that they are innocent, claiming that the administration and DOJ are merely targeting them for retaliation.

US District Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. But she also left the door open for the federal authorities to refile the case.

• Judge dismisses charges against ex-FBI director Comey and NY attorney general James
• Federal judge states government 'missteps' may have compromised Comey case
• What are ex-FBI director James Comey charged with?

Comey admitted that possibility after the ruling, stating he believes Trump is likely to target him once more.

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

But the DOJ faces steep hurdles to effectively try both after this setback, and experts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

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

Might the justice department 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 pursue this option, pledging to use all legal means, including an immediate 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.

Abbe Lowell, James's lawyer, vowed to continue to challenge any additional 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 involvement in the appeal unclear.

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with lying to lawmakers and obstruction of justice. Government lawyers charged Letitia James with bank fraud and providing false information to a bank.

Both pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, both also claimed to be targets of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the government might try to assemble fresh grand juries and secure new indictments.

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

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

I can tell you it will be hotly contested, whether Comey's case can be re-indicted if a properly assigned attorney is assigned and is can obtain an indictment.

He characterized the complex web of attorneys, courts, and legal filings involved as a legal quagmire with no easy solutions.

It might be more difficult for the government to try to bring the identical accusations against Comey.

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

Still in that situation, his lawyers said it plans to argue the government 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 on Monday.

What is the fate of prosecutor Lindsey Halligan?

In the pair of rulings on the charges against James and Comey, the judge was blunt: Halligan's appointment was improper.

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

Therefore, she lacked legal power to present the indictment, the judge wrote.

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

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

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

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

The administration maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.