The who, what, where, and why of the Trump administration’s first major scandal – Michael Flynn’s ignominious resignation on Monday as national security adviser – have all been thoroughly discussed. Relatively neglected, and deserving of far more attention, has been the how.

The fact the nation’s now-departed senior guardian of national security was unmoored by a scandal linked to a conversation picked up on a wire offers a rare insight into how exactly America’s vaunted Deep State works. It is a story not about rogue intelligence agencies running amok outside the law, but rather about the vast domestic power they have managed to acquire within it.

We know now that the FBI and the NSA, under their Executive Order 12333 authority and using the Foreign Intelligence Surveillance Act as statutory cover, were actively monitoring the phone calls and reading text messages sent to and from the Russian ambassador to the United States, Sergey Kislyak.

Although the fact of being able to monitor any specific individual is classified TOP SECRET, with the Special Intelligence (SI) caveat, and cannot be released to foreigners, the existence of this monitoring in general is something of an open secret, and Kislyak probably suspected he was under surveillance.

But a welter of laws, many of them tweaked after the Snowden revelations, govern the distribution of any information that is acquired by such surveillance. And this is where it’s highly relevant that this scandal was started by the public leaking of information about Mike Flynn’s involvement in the monitoring of Kisylak.

The way it’s supposed to work is that any time a “U.S. person” – government speak for a U.S. citizen, lawful permanent resident, even a U.S. company, located here or abroad – finds his or her communications caught up in Kislyak’s, the entire surveillance empire, which was designed for speed and efficiency, and which, we now know, is hard to manage, grinds to a halt. That’s a good thing. Even before Snowden, of course, the FBI would “minimize” the U.S. end of a conversation if analysts determined that the calls had no relevance to a legitimate intelligence gathering purpose. A late night call to order pizza would fall into this category.

But if the analyst listening to Kislyak’s call hears someone identify himself as an agent of the U.S. government – “Hi! It’s Mike Flynn” certainly qualifies – a number of things have to happen, according to the government’s own rules

At this stage, the actual audio of the call and any transcript would be considered “Raw FISA-acquired information,” and its distribution would be highly restricted. At the NSA, not more than 40 or so analysts or senior managers would be read into the classification sub-sub compartment that contains it, called RAGTIME-A, B, C, D or P, where each letter stands for one of five different categories of foreign intelligence.

For anything out of the ordinary – and this qualifies, at the FBI –the head of the National Security Division would be notified, and he or she would bring the raw FISA transcript to FBI Director James Comey or his deputy. Then the director and his deputy would determine whether to keep the part of the communication that contained Flynn’s words. The NSA has its own procedures for determining whether to destroy or retain the U.S. half of an intercepted communication.

In this case, there were three sets of communications between Flynn and Kislyak, at least one of which was a text message. The first occurred on Dec. 18. The last occurred on Dec. 30, a day after sanctions were levied against people that the Russian ambassador knew – namely, spies posing as diplomats.

The factors FBI Director James Comey and his deputy would have had to consider in this case are complex. Flynn was a former senior intelligence official not in power at the time of the communications, though he did have an interim security clearance. Then there was the policy context: The United States wanted to know why Russia decided not to retaliate, according to the Washington Post.

But the most important factor would have been that Flynn was talking to the ambassador of a country who has been credibly accused of interfering in the election of his boss. Regardless of the content of Flynn’s side of the call, it would be negligent if the FBI decided to minimize, or ignore, these calls, simply because Flynn is a citizen who is not subject to surveillance himself. But what Flynn said in the calls would have played a role in the FBI’s determination to keep the transcripts unminimized – a fancy way of saying “unredacted.”

The Justice Department would then decide whether to pursue the matter further. If they thought Flynn was acting as an agent of a foreign government – and there’s not a gram of evidence for this – they could apply for a normal surveillance warrant under Title III of the U.S. code.

It is rare for the FBI or NSA to distribute raw, unminimized FISA material outside of controlled channels. But given the intelligence questions at stake, they would have had an obligation to circulate the Flynn transcripts to the National Security Council, which, during most of January, was peopled with President Obama’s staff and detailees from other government agencies.

Sometime before Jan. 12, the fact that these conversations had occurred was disclosed to David Ignatius, who wrote about them. That day, Sean Spicer asked Flynn about them. Flynn denied that the sanctions were discussed. A few days later, on Jan. 16, Vice President Mike Pence repeated Flynn’s assurances to him that the calls were mostly about the logistics of arranging further calls when Trump was president.

At this moment, we are four days away from Trump’s inauguration. The FBI agents and analysts who monitored the calls, as well as some NSC officials in the Obama administration, along with a few senior Justice Department attorneys, all knew with certainty that the content of the calls contradicted Flynn’s account of them. The transcript of the Dec. 30 call proved as much.

For reasons unclear to us, Comey did not believe that Flynn’s misrepresentations amounted to a sufficient national security risk on Jan. 16 to spring FBI investigators on the Trump team, or even on Flynn. Perhaps he felt that doing so right before the inauguration would have been too unseemly.

But he did want to know more. In an extraordinary turn, agents were sent to the White House to interview Flynn just a few days after Trump was sworn in, according to the New York Times. We don’t know what they learned. But by Jan. 26, Comey had dropped his objections to notifying the White House. (In the interim, Sean Spicer was asked about the calls again, and repeated the Flynn untruth.)

Acting attorney general Sally Yates informed the White House counsel, Don McGahn, that their account of what Flynn said did not match what Flynn insisted he said.

McGahn had the clearance to see the transcript, but it’s fair to assume that many members of Trump’s team probably did not. But that does not explain why it took 11 days for Pence, who certainly did have such clearance, to learn about the Justice Department warning. And it does not explain what the White House was doing as it mulled over this information for weeks.

Here we have to leave the realm of reasonable conjecture, but the best explanation might be the easiest: incompetence or ineffectiveness from the White House counsel, and an inability to foresee the real world consequences of their own decisions by White House principles. The country’s intelligence agencies, by contrast, were far-more clear-sighted in the use of their prerogatives and power.

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