Frida Ghitis is a world affairs columnist for The Miami Herald and World Politics Review, and a former CNN producer and correspondent. The views expressed in this commentary are her own.

(CNN) If President Donald Trump's administration thinks that Mike Flynn's departure from his post as national security adviser will bring an end to the scandal that ended his tenure, it is about find out that just the opposite is true. This crisis is not over; it's only beginning.

Trump and his close White House circle wanted Flynn to fall on his sword, taking the blame for inappropriate and possibly illegal telephone conversations he held with Russian Ambassador Sergey Kislyak during the transition period. In those calls, Flynn reportedly reassured Moscow that sanctions imposed by President Barack Obama over Russia's hacking of the US election would be lifted by the incoming administration.

When news of the phone calls became public , and as recently as a week ago Wednesday, Flynn vehemently denied he had discussed sanctions -- and the denials were repeated by press secretary Sean Spicer and by Vice President Mike Pence . We now know that version of events was false. That brings to mind one of America's most poignant political history lessons: The cover up is worse than the crime, a legacy from the Watergate scandal that brought down a president.

In this case, however, even if there had been no cover up of what transpired during those calls, there are reasons for concern.

The official line is that Flynn "misled" the vice president and other administration officials. But that, remember, comes from an administration fond of "alternative facts." We don't know if the denials were due to Flynn giving " incomplete information ," as he described it, to his colleagues, or were simply talking points created by White House political operatives. The larger more important suggestion tacitly embedded in the administration's new version of events is that Flynn was a rogue national security adviser, who was freelancing when he contacted an official from a hostile foreign government, rather than a team player implementing approved policy. According to their preferred version, Flynn's departure severs the rotten limb, solving the problem.

But the fact is that the only reason Flynn's phone calls made headlines is because they involved Russia. And when it comes to Russia and the Trump administration, Americans are deeply suspicious, and justified in their doubts. Since early in his presidential campaign, Trump's pronouncements regarding Russia were raising eyebrows, as he suggested lifting sanctions and radically transforming policies that had strong bipartisan support.

When Trump brought to his campaign Paul Manafort, a man with close and controversial ties to powerful interests in Russia, it heightened concerns about links to that country. And when the campaign pressured the Republican party to scrub its platform of criticism of the Kremlin and support for Ukraine, those concerns appeared to be borne out.

Later, US intelligence agencies concluded that Russia had interfered in the US election seeking to help Trump win the presidency. Not long after that, news emerged of a secret dossier compiled by a former British intelligence officer, claiming that Trump surrogates and Russian officials had worked together to help the Trump campaign. The charges -- many still uncorroborated -- added to the questions surrounding the Trump team and Russia.

That is why the Flynn phone calls resonated. If Flynn had conducted legally problematic telephone conversations with the ambassador of just about any other country on Earth, the matter would probably have died. But promises of lifting sanctions against Russia touched a very sensitive nerve.

Flynn's departure after just three weeks in office is a dramatic political blow to the administration, but it will do nothing to make the issue disappear.

To the contrary, it adds urgency to the matter. After all, there is no proof that the phone calls were an independent, unauthorized activity, and talk of lifting sanctions -- the subject of the conversations -- fits neatly with Trump's controversial pronouncements on the campaign trail. On its face, it also jibes with the rest of the sordid Russian interference in the election.

This is not to say that Flynn's departure is a meaningless development. The loss of a top aide during the first month of the new presidency is a hard-to-scrub stain on the administration. And when that official is the controversial Mike Flynn, the move is hardly inconsequential.

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Trump critics can rightly rejoice in knowing that Flynn will no longer sit near the Oval Office. Flynn has a track record that includes not only questionable dealings with Russia , but also a troubling inability to distinguish between Islamic radicals and everyday Muslims . Most disturbing of all, in my view, has been Flynn's appetite for bizarre conspiracy theories . When the top national security adviser to the US President believes outlandish internet rumors enough to personally disseminate them over social media, it is no exaggeration to say it puts the world at risk. That particular risk, thankfully, is now removed, or at least lessened.

Flynn's odd relationship with reality was on display until the last moment, when he tendered his resignation saying he was honored to have served , "in such a distinguished way." It was an oddly Trumpian, self-congratulatory characterization of a record-short stint that ended in disaster.

It was hardly helpful to Flynn or to the Trump administration that members of the Russian parliament mounted a fierce defense of the fallen adviser. In both chambers of the Russian parliament, the heads of the foreign affairs committees defended Flynn, decrying what they view as paranoia about Russia spreading in the United States.

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For both Trump and Russian President Vladimir Putin, the continuing storm surrounding their relationship means sanctions are unlikely to be lifted any time soon. If Trump removed the sanctions in this environment it would amount to pulling the pin on a political grenade.

There is, of course, a way to ease the paranoia. But that will require putting the Trump-Putin relationship under the microscope. Something Trump perhaps would rather avoid.

Flynn's fall does nothing to ease Trump's Russia-related political crisis. It is just one more marker along a road leading the Trump presidency to an uncertain destination.