But this is not a normal presidency, and Donald Trump’s team did not run a normal transition. Nor do normal national security advisers start their tenure as reported objects of investigations. As Michael Flynn took on his role in the Trump administration, the U.S. intelligence community had already unanimously concluded that Russian hacking, and Russian trolling, played a role in the presidential election. But the question of whether Flynn, Trump or anyone else had promised the Russian government something in exchange for that help remained wide open.

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In that context, a normal phone call became a potential scandal — and Flynn knew it. So, clearly, did many others — including the president. The call may not necessarily be the smoking gun, the ultimate “proof” that there was a quid pro quo: “You help us with the election, we help you by lifting sanctions.” But it sure looks like it could be.

That explains why Flynn lied about the call to the vice president, and to the press. That explains why — although he has known about this issue for many weeks — the president did not fire Flynn earlier. That also explains why the president has expressed regret about the leak of the transcript of the call but not about the fact that Flynn made the call in the first place. That also explains why Flynn resigned. He knows, and the president knows, exactly why this looks bad.

Finally, the Flynn resignation helps put another mystery in context: Why didn’t Trump lift sanctions on Russia during his first week in office? Many in Washington, and certainly in the State Department, believed he was about to do so; many Europeans were already preparing their response. Supposedly, he dropped the idea of an executive order because of pressure from Senate Majority Leader Mitch McConnell (Ky.) and Sen. John McCain (R-Ariz.), and because British diplomats persuaded his team not to do it right before the visit of the British prime minister.

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Now we know that there could have been another reason: Trump, and Flynn, were beginning to worry about how it would look — to the investigators focusing on Flynn, as well as to others who knew about the content of Flynn’s call — if they appeared to reward the Russian government for its assistance. Or, of course, how it would look if they really had rewarded the Russian government for its assistance.

The investigation continues.