Elie Honig is a CNN legal analyst and former federal and state prosecutor. The views expressed in this commentary are his own. View more opinion on CNN. Watch Honig answer readers' questions on "CNN Newsroom with Ana Cabrera" at 5:40 p.m. ET Sundays.

       (CNN)Just when it seemed that Attorney General William Barr would get away with intentionally tanking his own Justice Department's conviction of President Donald Trump's former National Security Adviser Michael Flynn, a federal judge on Wednesday slammed on the brakes and now is demanding real answers.

       There's a common saying that the courts are the final bulwark against tyranny. "Tyranny" may be a bit much here, but Judge Emmet Sullivan certainly seems to be taking a stand against an unconscionable abuse of power by Trump and Barr.

       Barr's move to clear Flynn is outrageous and transparently political. Flynn pleaded guilty to lying to the FBI about his contacts with the Russian ambassador during the presidential transition. He admitted under oath that he knew it was a crime to lie to the FBI, that he was not entrapped, that he was "in fact guilty of the crime charged," and that he had committed additional crimes relating to his work for Turkish interests in the United States.

       According to a letter signed by over 2,000 former federal prosecutors and other Justice Department alumni (including me), it is "extraordinarily rare, if not unprecedented" for the Justice Department to move to vacate a conviction after such an admission of guilt by a defendant. With this move, Barr once again undermined his own credibility and independence.

       I signed the call for William Barr to resign. This is why

       Nonetheless, given that both parties before him -- Flynn and the Justice Department -- agreed that the case should be thrown out, Judge Sullivan easily could have issued a one-line ruling and been done with it: "Both parties concur, case dismissed." But Judge Sullivan, an experienced and savvy jurist with a reputation as a "fiercely independent thinker," according to The Hill, sensed something was amiss and refused to take the easy way out.

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       Instead, the judge -- clearly skeptical of both Flynn and the Justice Department -- has taken the unusual step of calling on interested outside parties ("amicus curiae," in legal lingo) to submit briefs. And Judge Sullivan has appointed a former federal judge, John Gleeson, to review the case and provide recommendations.

       It seems clear where this is headed. If Judge Sullivan had bought Barr's position, he would have tossed the case by now. I expect Sullivan's deeper inquiry will reach the same conclusion as I have: that Barr's effort to dismiss the Flynn case is a political gambit unjustified by the facts or the law.

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       If that happens, it will be a devastating rebuke to Barr. And such a result would cut the legs out from the dubious claim that members of the Obama administration somehow improperly "unmasked" Flynn (when in fact "unmasking" is a routine part of intelligence work, and there is no evidence of improper political motivation).

       The question now is whether Trump will preempt the damage by pardoning Flynn. A pardon would, of course, end the Flynn case and prevent Judge Sullivan from formally rejecting Barr's motion and proceeding to sentence Flynn. But make no mistake: if Trump does pardon Flynn now, it's as good as an admission that he and Barr got caught trying to cheat the system. Final bulwark, indeed.

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