SOME resignations from high office are like the cauterising of a wound: brutal but decisive. Others resemble a battlefield amputation: a painful loss which cannot dispel the sinister whiff of some deeper infection. As Washington, DC absorbs the news, just before midnight on February 13th, that Michael Flynn has quit as National Security Adviser to President Donald Trump after less than a month in office, an ominous note lingers in the air. There is something unhealthy about the way this new government operates.

Mr Flynn, a retired three-star general and former chief of a Pentagon spy agency, had to quit after admitting that he had misled Vice-President Mike Pence about his contacts with a Russian envoy after the November presidential election but before the inauguration in January, when Mr Flynn was still a private citizen. That inaccurate briefing had left Mr Pence to head out onto television and unwittingly spread false information as he defended the man who on January 20th became head of the National Security Council. In his half-contrite, half-defiant resignation letter, Mr Flynn wrote of having sincerely apologised to both Mr Pence and Mr Trump for “inadvertently” misleading them with “incomplete information”.

Mr Flynn had always been tipped as a likely first casualty of the Trump administration. He made few allies with his manner, described as an unhappy blend of grievance, anger and arrogance. His resignation letter spoke of feeling honoured to have served his country in such a “distinguished” post, if only for three weeks. When trusted by a president, the national security adviser holds an immensely powerful job, as gatekeeper, referee, enforcer and co-ordinator whenever questions of defence, foreign policy and national security reach the White House for a presidential decision.

Visitors to White House meetings had reported, with surprise, how much the angular, rail-thin general seemed to grate on his boss, the president. That was even though Mr Flynn had the great advantage, in this administration, of having being one of the first high-ranking figures to endorse Mr Trump, startling his brother officers by leading a chant against Hillary Clinton of “Lock Her Up” at the Republican National Convention in 2016.

In the end, Mr Flynn suffered death by a thousand leaks. Former Obama administration high-ups and still-serving career intelligence officials told reporters, notably at the Washington Post and New York Times, that the general had been overheard by American spooks talking by telephone to Russia’s ambassador to America, Sergey Kislyak, in December, in the dying days of the Obama era. Though Mr Flynn claimed that those contacts had been anodyne, turning on the logistics of future meetings and conversations, allegations spread that the pair had in fact discussed sanctions imposed by the Obama administration to punish Russia for meddling in the November presidential election, notably by stealing and leaking the private e-mails of senior officials in the Clinton campaign and Democratic Party.

Specifically, the word was that Mr Flynn urged the Russians to be patient and wait for Mr Trump to take office, and not to overreact to the sanctions. That allegation was all the more explosive because Mr Flynn already faced questions about ties with Russia after being fired by President Barack Obama as head of the Defense Intelligence Agency (DIA). Mr Flynn left that agency in 2014, claiming that he was fired for raising uncomfortable questions about the Obama government’s approach to fighting Islamic terrorism (Team Obama called him an insubordinate, obsessive and bad manager). In 2015 the former DIA chief turned up in Moscow at a gala for the state propaganda outlet, Russia Today, sharing a table with President Vladimir Putin.

In theory, Mr Flynn’s contacts with the Russian ambassador in December of last year were a potential breach of a law, the Logan Act, which bars private citizens from conducting foreign policy. But nobody has ever been convicted under the Logan Act. As so often in Washington, the cover-up was worse than the crime. And for critics of the Trump White House, it is that cover-up which seems to give off a gangrenous smell.

For the list of officials who must have known about Mr Flynn’s contacts with the Russian ambassador—a man whose phone calls are routinely intercepted, a fact known to every spy in Washington—is not short. Hours before Mr Flynn’s resignation, even as some senior aides to Mr Trump insisted that the general enjoyed the president’s full confidence, the Washington Post reported that a senior official at the Justice Department had briefed Team Trump in January that they believed that Mr Pence had been misled about Mr Flynn’s Russian contacts. The Post’s sources went further, saying that officials “couldn’t rule out that Flynn was acting with the knowledge of others in the transition.”

Before parting ways Mr Flynn and Mr Trump shared a belief that Mr Putin’s Russia might be a valuable—and usefully unsqueamish—ally in the fight against global Islamic extremism, a fight that Mr Flynn has cast in apocalyptic terms, as a clash of civilisations between Islam and the West.

Relations between Team Trump and the press are already rotten. They will not be helped one bit by the role of the media in taking down Mr Flynn, or—in the other direction—by days of official denials and obfuscation about the fate of the national security adviser. The atmosphere among officials who serve the president, including in the National Security Council, is also rotten. Career officials seconded to the NSC and White House talk of a policy machine paralysed by infighting and distrust. Political appointees brought in by Mr Trump have formed into warring factions, pitting establishment Republicans, such as the chief of staff, Reince Preibus, against radical nationalists with Mr Trump’s ear, such as Stephen Bannon and Stephen Miller. All sides are briefing against each other.

The acting national security adviser is another retired three-star general, Keith Kellogg. Possible permanent replacements are rumoured to include David Petraeus, the former four-star commander and architect of a successful counter-insurgency “surge” in Iraq. Optimists will see a chance for Mr Trump to reset his national-security apparatus after a false start. The president has, after all, hired a distinguished and principled former marine general, James Mattis, to be his defence secretary, and chosen as his secretary of state Rex Tillerson, an accomplished former boss of ExxonMobil, the energy giant. Pessimists will worry that Mr Flynn’s departure is not enough to cure what ails this administration.