It’s often seemed in recent weeks that President Donald Trump and special counsel Robert Mueller are headed for some sort of showdown.

And if so, Trump’s new chief of staff, John Kelly, will have a major role in determining just how that confrontation plays out.

In his effort to rescue Trump’s failing presidency, Kelly will have to deal with many difficult problems, from warring advisers to leaks to an incoherent policymaking process to the presidential Twitter account.

But the most bedeviling challenge he’ll face may be dealing with the president’s own instincts on the Russia scandal — specifically, his repeatedly expressed desire that Mueller’s investigation go away.

It’s clear that Trump would very much like this investigation to disappear, and that he has little respect for niceties about the rule of law that would hold him back. He’s already tried to get then-FBI Director James Comey and other officials to “lift the cloud” of the Russia probe. He then fired Comey. He’s publicly berated Attorney General Jeff Sessions for recusing himself. He’s warned Mueller not to investigate his businesses. And he’s reportedly musing about firing Mueller.

“Like Nixon, there is little chance that Trump will change in any fundamental way,” writes Julian Zelizer, a professor of history at Princeton. “With each of Trump's tweets and bombastic rally statements, Kelly will discover it is increasingly difficult to ‘reset’ the situation.”

But intriguingly, a new CNN story suggests Kelly may not be so eager to play ball. Shimon Prokupecz and Pamela Brown report that after Comey was fired, Kelly called him, expressed his unhappiness with Trump’s move, and said he was considering submitting his own resignation in protest.

Kelly may well try to convince Trump not to put the rule of law at risk by going after Mueller — though that could earn him the ire of a president obsessed with loyalty above all else. Alternatively, and more troublingly, he could end up following the chain of command to carry out his boss’s evident wishes and try to make the investigation disappear.

We don’t yet know which path Kelly will choose. But Trump’s own instincts around several different fronts of the Russia scandal — from public disclosures to the fate of Sessions to the fate of Mueller’s investigation itself — would prove enormously challenging for any staff to deal with.

Trump’s desire to deceive the public is causing him political and legal problems

If you want to know what sort of trouble Kelly may be headed into, take a look at a Washington Post report from Monday night.

The story revealed that when news about Donald Trump Jr.’s meeting with a Russian lawyer broke earlier this month, the president himself “personally dictated” the extremely misleading statement his son released in response. The statement about the meeting — which, per emails sent to Trump Jr., was set up with the promise of Russian government–sourced dirt on Hillary Clinton — claimed it was “primarily” about adoption policy.

The Post’s report makes clear that, in least at this case, President Trump himself dictated a strategy of deceiving the public about his associates’ contacts with Russia. And advisers to the president told the paper that Trump “is increasingly acting as his own lawyer, strategist and publicist, often disregarding the recommendations of the professionals he has hired.”

The president’s bad instincts here caused political problems for him — since Trump Jr.’s first misleading statement soon spurred leaks contradicting him, prolonging the story for days and making the facts seem even worse when they did emerge.

And they may cause Trump legal problems too. Special counsel Robert Mueller, who is reportedly investigating whether the president has tried to obstruct justice, seems very interested in all this. CNN reported last week that he had sent a request to the White House to preserve documents not only about the Trump Jr. meeting itself but about “any decisions made regarding the recent disclosures about the June 2016 meeting.”

Enter John Kelly. He will now have to choose how to handle disclosures of any other Russia-related information that he learns about — even though the president has made clear that his preference is to obfuscate and deceive. Kelly will have to decide whether to help him do that, or push back.

The fate of Jeff Sessions remains unresolved

Or take the still-unresolved public drama over the fate of Attorney General Jeff Sessions.

Since March, Trump has reportedly been furious that Sessions recused himself from oversight over the Russia investigation. In recent weeks, that fury spilled out into public view, with the president openly criticizing and belittling his attorney general in interviews with reporters and on Twitter.

In one sense, it appears to be a rather crude attempt to provoke Sessions to resign — something that probably not coincidentally would allow Trump to appoint a new and un-recused attorney general.

But Trump also has angrily and repeatedly claimed Sessions’s Justice Department isn’t sufficiently investigating Hillary Clinton and Democrats. He seems to genuinely want the federal government’s law enforcement power to be targeted against his political opponents rather than himself. And he’s said things to this effect enough times that he clearly isn’t going to forget about it.

Again, Kelly has a role to play here. As a former Cabinet secretary who likely has some sympathy for Sessions’s plight, he may try to convince the president to stop publicly berating the attorney general and respect Justice Department independence — even though Trump clearly doesn’t want to.

Alternatively, Kelly could end up trying to achieve the president’s evident goal of bringing DOJ more in line with his personal whims — whether by pushing out Sessions or by other means.

And then there’s Robert Mueller

All of this may be stage-setting for the real showdown much of Washington has been expecting for months now — Trump’s desire to end or at the very least rein in Mueller’s investigation.

The president has already fired FBI Director Comey, and admitted that the Russia investigation was one reason he did so. That ended up backfiring when Mueller was appointed as special counsel to take over the probe.

Since then, Trump has naturally aimed a torrent of criticism at Mueller too, claiming the investigation is biased against him and openly warning Mueller not to move far away from Russia-related matters.

And behind closed doors, Trump has reportedly mused about firing Mueller — something that would be difficult and likely mean the resignation of many Justice Department officials, but could well happen if Trump feels threatened or aggrieved enough by the investigation.

So how will Kelly handle Trump’s unhappiness with the special counsel? The question is particularly interesting given CNN’s report that Kelly called Comey to express sympathy over his firing and even suggested that he might resign in protest too.

If that report is accurate and Kelly does intend to stick to those principles, he’ll certainly have a tough road ahead in this White House. Trump clearly believes this investigation is a major threat to his presidency — indeed, as his tossing of longtime loyalist Sessions under the bus shows, he may well view it as more important than the rest of his policy agenda now.

So Trump will inevitably judge Kelly on how he handles the Russia investigation threat. And Kelly will face his own difficult challenges in dealing with the president’s troubling instincts on this topic. It’s a situation that doesn’t seem likely to end well.