Over the weekend, I wrote a piece called Flynn and Kislyak’s Israel Talks Were a Bigger Deal, by which I meant that the Flynn-Kislyak communications on December 22nd about the anti-settlers U.N. resolution were more troubling than their December 29th communications about the expulsion of thirty-five Russian “diplomats.” My basic point is backed up by Daniel Hemel and Eric Posner in a New York Times opinion piece this morning called Why the Trump Team Should Fear the Logan Act. As they argue persuasively, if the Logan Act has any legitimate application at all, it must be appropriate in a situation where someone has both the power and the influence to actually undermine the U.S. government’s position on a U.N. Security resolution.  Flynn did not succeed in convincing Russia to veto or force the delay of the resolution, but the Trump team did succeed through other means in forcing a temporary delay.

It should be noted here, though, that the egregiousness of what the Trump team did to undercut the government’s position on the U.N. resolution had nothing in particular to do with Russia.  Flynn was instructed to contact all fifteen members of the U.N. Security Council, and Russia was on that list because they’re a permanent member, not because of anything they might have done to help Trump get elected.  Flynn lied about discussing sanctions with Kislyak because it would have looked incriminating in light of the release of the Steele Dossier and the declassification of the Intelligence Community’s report on Russian hacking. He lied about asking Russia to veto or delay the U.N. Resolution because it was a potentially criminal violation of the Logan Act.

That’s not to say that the Logan Act wasn’t implicated in the sanctions conversations, but it was a less obvious and more defensible violation because Flynn didn’t ask Russia to do anything beyond showing restraint.

These are distinctions largely missed by Byron York. For him, the FBI would never have questioned Michael Flynn on January 24th if they weren’t relying on the Logan Act as their justification. And, since the Logan Act has never been successfully prosecuted and is considered of suspect constitutionality, it was really a dirty trick to use it to trip up the incoming administration from the get-go.

I think York would be on fairly solid ground if he were only talking about the conversations Flynn had with Kislyak on the U.N. Resolution. In that case, the problem was clearly that an incoming administration was working with foreign powers to undermine official U.S. policy. The latter communications, however, were related to an ongoing counterintelligence investigation.

The working theory of that counterintelligence investigation was that the Trump campaign was actively working with the Russians. The scope of the scheme was also under investigation, so it may have initially been about winning favor with the Russians for some land development projects and then morphed into assistance in winning the general election. The Russians may have, at first, only been hoping that Trump would bloody Jeb Bush and other neoconservatives and introduce a more pro-Russian narrative into the Republican primaries. Once Trump secured the nomination, it appears to have pretty promptly moved to efforts to gain sanctions relief. This can be seen in the timeline in a variety of ways, including the hiring of Paul Manafort, the staffing of Trump’s foreign policy team with Kremlin sycophants, the meeting in Trump Tower where dirt on Hillary was discussed in the context of sanctions relief, and the softening of the Republican platform with regard to arming Ukraine.

The intelligence community sought FISA warrants and eventually secured at least one in their efforts to track members of the Trump team who were meeting with known or suspected Russian intelligence officers and agents. Michael Flynn was under suspicion throughout this period, especially after he went to Moscow and feted Vladimir Putin at the RT network’s 10th anniversary gala.

So, when the FBI decided to take the bold step of questioning the National Security Advisor on his fourth day on the job, it wasn’t because they were primarily concerned with Logan Act violations. It wasn’t even necessarily the criminal element they were focused on, since a counterintelligence investigation need not lead to criminal charges.

To get an idea of what Byron York entirely missed in his retelling of this history, consider that the following was published the day before Flynn was forced to resign:

For the past three weeks, according to a former National Security Agency (NSA) analyst and counter-intelligence officer, some the America’s spy agencies have begun withholding intelligence from the Oval Office amid fears “the Kremlin has ears inside” the White House situation room.

The claims follow reports that National Security Adviser Michael Flynn discussed lifting sanctions against Moscow with a Russian diplomat before Mr Trump took office.

An NSA official told the New York Observer it was holding back some of the “good stuff” from the White House, while one Pentagon worker said: “There’s not much the Russians don’t know at this point. Since January 20, we’ve assumed that the Kremlin has ears inside the [situation room].”

If Flynn hadn’t already been the subject of a counterintelligence investigation for more than a year when he took his position in the White House, his conversation about sanctions with Ambassador Kislyak might very well have been interpreted in terms of its relationship to the Logan Act. In reality, Kislyak was seem as a point man for contacts with the Trump team. In this same time period, Jeff Sessions was exposed for having met with Kislyak in his private Senate chambers, knowledge of which surely came from these same counterintelligence investigators. Flynn and Kislyak were already suspected of being conspirators long before their December conversations were monitored.

The intelligence community felt confident enough that Flynn was compromised that they considered him the Kremlin’s “ears inside the Situation Room” and began withholding intelligence from the White House.

Now, we can talk about statutes and legal precedence all we want, but the reality is that on January 24th when the FBI questioned Michael Flynn, they considered him a likely Russian spy. They considered the National Security Advisor of the United States to be a spy for the Kremlin. If we don’t have laws for rectifying that situation, we need to invent them.

Now, a normal president who was presented with evidence and worrisome suspicion that his top foreign policy advisor was a Russian spy might behave in a number of ways, but you’d think ultimately that they’d want to get to the truth of the matter. He’d either want to satisfy his own intelligence community that their suspicions were meritless or he’d want to remove that person and discover how he’d so successfully won his trust.

But Trump is not a normal president and he had reacted with dismissal and contempt to every warning the intelligence community tried to provide him in briefings throughout the campaign. This made it appear that Trump was complicit and himself compromised, but that wasn’t something so easily solved.

To fix that problem required that the counterintelligence investigation continue and bear fruit.

So, this is the context in which FBI director James Comey received Trump’s requests that he drop the Flynn matter and reassure the public that there was nothing to Trump’s collusion with the Russians. He wasn’t going to do those things and they were further evidence that the intelligence community was correct to be wary of the new president’s loyalties.

Now, let’s consider how this looks:

President Trump told Russian officials in the Oval Office this month that firing the F.B.I. director, James B. Comey, had relieved “great pressure” on him, according to a document summarizing the meeting.

“I just fired the head of the F.B.I. He was crazy, a real nut job,” Mr. Trump said, according to the document, which was read to The New York Times by an American official. “I faced great pressure because of Russia. That’s taken off.”

Mr. Trump added, “I’m not under investigation.”

The conversation, during a May 10 meeting — the day after he fired Mr. Comey — reinforces the notion that the president dismissed him primarily because of the bureau’s investigation into possible collusion between Mr. Trump’s campaign and Russian operatives. Mr. Trump said as much in one televised interview, but the White House has offered changing justifications for the firing.

Does that sound kosher to you? Does it seem criminal? Problematic for our national security?

But it has nothing to do with the Logan Act, does it?

So, yes, the Trump team should be worried about the Logan Act but this has never been about the Logan Act. It’s far more serious than that.