ANALYSIS: Flynn resignation raises dark questions surrounding Trump and Russia

There are Washington resignations that end stories. Then there is the resignation of National Security Adviser Michael Flynn.

Flynn's abrupt departure reveals a national security team in disarray at a time when President Trump is being tested by friends and foes alike. With demands for answers and investigations only increasing, the story goes significantly deeper than questions of who is in charge and who knew what and when.

The circumstances of Flynn's exit raise the most delicate and dark brand of questions for the White House he wound up serving only briefly. They revive questions of alleged Russian interference with the presidential election, demanding inquiries that could lead to far more serious revelations about the president and his inner circle.

Sen. John McCain, R-Ariz., who is rapidly emerging as the most influential counterweight to the administration on Capitol Hill, said Tuesday there is "significant disarray" in the national security realm. He made the connection that has Washington fixated on a series of bigger pictures.

"Gen. Flynn's resignation also raises further questions about the Trump administration's intentions toward Vladimir Putin's Russia," McCain said.

It's not just intentions but connections that figure to drive the story. The extent of the Trump operation's communications with Russian operatives during the election has been the subject of widespread speculation but few verifiable details so far.

Now Flynn is admitting to calls - plural - with the Russian ambassador to the U.S., without providing information on the timing. When it comes to the content, it's now established that he misled even Vice President Mike Pence about whether the topic of lifting sanctions came up during the transition period, after the then-current administration imposed new sanctions in retaliation for apparent Russian attempts to influence the election.

It's not yet established whether Flynn misled the president or whether Trump knew sanctions were being discussed with the Russians before he took office. It's also not known whether Flynn or other Trump campaign or administration officials had similar conversations or discussed other topics in backchanneling to the Kremlin.

There are questions for the Department of Justice: Will Flynn be prosecuted for freelancing foreign policy without authority? Will a special counsel oversee FBI inquiries into the Trump team's contacts with the Russians?

Recall that new Attorney General Jeff Sessions was a regular alongside Flynn on the campaign trail. Flynn led chants of "Lock her up" at the Republican National Convention and declared, regarding Hillary Clinton, "If I did a tenth, a tenth of what she did, I would be in jail today."

There are questions for Congress: Will Republican watchdogs be as interested in this as they were in probing advocacy of Ivanka Trump's product line, to say nothing of Benghazi or email servers? Will they resist Democratic calls for a bipartisan House-Senate investigation?

There are questions for the White House: Who knew of Flynn's deception? Why did it take so long (three weeks from the time the then-acting attorney general told the White House counsel about it) for Flynn to go? And after all that, was he fired, or was he truly allowed to resign?

Who is running the national security team now? Were any precautions put in place to guard against the possibility that the Russians would take advantage of the fact that Flynn discussed lifting sanctions? Can and will sanctions be lifted now, given what is known about backchannel communications?

For Trump, Russia has loomed large for nearly the entirety of his brief political career. The bear is just getting bigger.