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Two high-profile critics of President Trump achieved significant legal victories on the start of the week when a federal judge dismissed the federal indictments against them.

Over recent weeks following their charges, former FBI Director James Comey and NY AG Letitia James have insisted fiercely that they are not guilty, claiming that the president and justice department are merely targeting them for retaliation.

US District Judge Cameron Currie dismissed the charges against them due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. However, she left the door open for the government to try again.

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Comey admitted that likelihood after the decision, saying he believes the former president will probably come after him once more.

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

But the DOJ faces steep obstacles to successfully prosecute both after this setback, and legal analysts are reluctant to forecast what could happen next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, said Professor Kay Levine, law professor at Emory University.

Might the justice department challenge the ruling?

The Department of Justice can challenge 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 indicated she would take this route, vowing to use all legal means, including an expedited appeal.

Previously, the former administration has strongly challenged adverse decisions, taking cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

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

If there is an appeal, the DOJ likely would have its own lawyers argue the case, making Halligan's role in the appeals process unclear.

Is it possible there be new charges?

The federal prosecutors charged James Comey with lying to Congress and obstructing justice. Government lawyers indicted James with financial fraud and providing false information to a financial institution.

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

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

Based on my analysis, a new prosecutor could bring James' 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 the Comey matter.

It's clear that it will be hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is can obtain an charge.

He described the complex web of lawyers, judges, and motions involved as a legal quagmire with no easy solutions.

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

One problem is the statute of limitations – the deadline that government lawyers had to charge him for these specific allegations – which ended at the close of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the justice department to refile the case.

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

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

What is the fate of Lindsey Halligan?

In both decisions on the indictments against Comey and James, the judge was blunt: Halligan was wrongly appointed.

The judge stated in the James decision that the Attorney General's attempt to appoint Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

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

US attorneys are proposed by the president and require US Senate confirmation. US laws regulate how individuals can be assigned on a temporary basis, but the judge determined that Halligan's assignment had breached these regulations.

This makes Halligan's position on future cases against James and Comey, once more, 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 Halligan a special federal prosecutor and praised her work as excellent.

The administration maintained its position that Halligan's appointment was legal, spokesperson Karoline Leavitt told the press on Monday.