When Mike Flynn became National Security adviser he brought with him several long-time associates who had served with him in military assignments. Now one of them is gone.

A top deputy to National Security Adviser Michael Flynn was rejected for a critical security clearance, effectively ending his tenure on the National Security Council and escalating tensions between Flynn and the intelligence community.

The move came as Flynn’s already tense relationships with others in the Trump administration and the intelligence community were growing more fraught after reports that Flynn had breached diplomatic protocols in his conversations with the Russian ambassador to the United States.

On Friday, one of Flynn’s closest deputies on the National Security Council, senior director for Africa Robin Townley, was informed that the Central Intelligence Agency had rejected his request for an elite security clearance required for service on the NSC, according to two people with direct knowledge of the situation.

That forced Townley, a former Marine intelligence officer who had long maintained a top secret-level security clearance, out of his NSC post, explained the sources, who requested anonymity to discuss sensitive personnel matters.

One of the sources said that the rejection was approved by Trump’s CIA director Mike Pompeo and that it infuriated Flynn and his allies.

There could be an innocent explanation but that seems unlikely.

While it is conceivable that Townley had committed some act that warranted being rejected for a security clearance it seems farfetched. He had spent most of his adult life with high level clearances. It is hard to take this as anything but another phase of the war the CIA declared on Trump shortly after the election. The same organization had no problem granting the same kind of clearance to Ben Rhodes despite him having been declined a clearance by the FBI because of his slavish attachment to Iran. As the story says:

Both sources said that the CIA did not offer much explanation for why Townley’s request for so-called “Sensitive Compartmented Information” clearance was rejected. But the sources said that Flynn and his allies believe it was motivated by Townley’s skepticism of the intelligence community’s techniques — sentiments shared by Flynn.

“They believe this is a hit job from inside the CIA on Flynn and the people close to him,” said one source, who argued that some in the intelligence community feel threatened by Flynn and his allies. “Townley believes that the CIA doesn’t run the world,” the source said.

One can’t lose track of the fact that the CIA probably is less than happy with Flynn (it is hard to believe none of the sources for the Washington Post’s nothinburger yesterday were not CIA), knows it can’t get rid of him directly — that will come by the Death of the Thousand Cuts — and is just picking off his key allies.

Pompeo, of course, was between a rock and a hard place. He’s tying to gain control of an agency that is in open revolt against the administration and has demonstrated, now and under George Bush, that it is has no compunction about damaging a president and an administration if it believes its institutional prerogatives are in danger. Going along with sandbagging Townley is a small price to pay if it helps him avoid the Porter Goss treatment.