Vermont Senator Bernie Sanders and his wife are still in trouble with the FBI.

But it's the American people who are really in trouble.

A new report from a local Vermont publication, which has been all over the story, suggests that the FBI's probe of Jane Sanders for her role in alleged bank fraud is far from over. Witnesses are still being interviewed and a grand jury may soon be impaneled.

Sanders is in the middle of accusations that while she was president of Burlington College, she and other administrators misled bank loan officers about the real number of donations pledged to the college. Those false figures were used to secure a loan for a major campus expansion that flopped and led to the college's closing in 2016.

It first came to light back in May of this year that the FBI was looking into the matter, and had begun to do so while Barack Obama was still president. At the time, it was the first sign of trouble for Sanders' brand as an above-reproach progressive.

His political fortunes are now still in jeopardy. But beyond Bernie's future, this story is the latest example of the serious threat to the credibility of America's federal law enforcement system.

Back when this story first emerged, it was already something attorney Alan Dershowitz called a dangerous example of a tit-for-tat political use of the FBI to criminalize politics. At that point, it seemed like Dershowitz might be getting ahead of himself: It looks more like that assessment was on the money.

Now we know this probe is still going on, as is the widening and expanding scope of special counsel Robert Mueller's probe of alleged Russian collusion in the 2016 election.

It's not that the crimes or alleged crimes in these cases aren't important. But only the most naive observer would maintain these probes aren't at least somewhat politically motivated. And you'd have to be similarly naive not to notice that something has changed in American politics and federal law enforcement in the last several years.

What's changed is that an old deal that helped America avoid this kind of banana republic nonsense has been broken. Essentially, that deal went like this: Every four years, the voters got to choose the winners and losers in the national political arena. The winners got the spoils of power, and in return for the losers going away relatively quietly, they were mostly spared from politically-motivated legal punishment.

But then we learned in 2013 that the IRS was wrongly targeting conservative and Tea Party groups with audits and other bureaucratic red tape.

Then we had Hillary Clinton's refusal to go quietly after her election loss in 2016. She's spent much of the year since the election in full outcry mode, and even pushed out a new book complete with a national tour. Her refusal to slink off more quietly — as John Kerry, Michael Dukakis, Mitt Romney and others did — has led to a number of unique results. One of them is that new FBI Director Chris Wray hinted Thursday that Clinton could still be charged for her email scandal. That certainly looks like more tit-for-tat.

This was exactly the kind of broken deal that brought down President Richard Nixon. His attempted use of federal tools to punish his enemies and cover up his own crimes not only forced his resignation, but it came with overwhelming bipartisan approval at the time.

But with the growing perception at least by non-Democrats that the Mueller probe is tainted, it seems less likely any conclusion his team comes to will be accepted by any solid majority. The latest Rasmussen Reports poll shows that just 35 percent of Republicans and just 46 percent of independents believe Mueller is conducting an impartial investigation.

Those numbers seem likely to get a lot worse now that more stories about the partisan political activities of members of his team are leaking out. And polls like this are a brutal commentary on the current political climate as a whole.

Now none of us should shed any tears for Clinton, Jane Sanders or even Trump if they are found guilty of any real crimes. That's not the point. But it is worth crying over an entire set of federal law enforcement and regulatory agencies that are becoming less and less credible every day.

In the Sanders case, it's not that the probe should be dropped. But it is problematic that this relatively simple case involving just one small erstwhile college and a small bank is taking so long to resolve. It seems to have begun just as Senator Sanders was challenging then-President Obama's chosen successor, Hillary Clinton. It continues just as Sanders is becoming an enduring thorn in the current president's side.

This appears to make the probe's extended shelf life clearly more about politics than anything else. Love or hate Bernie Sanders, that's simply not right.

At some point in this dangerous game of chicken, someone needs to quit the political vendettas and put things right. That moment seems less likely to happen than ever right now.

Commentary by Jake Novak, CNBC.com senior columnist. Follow him on Twitter @jakejakeny.

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