His national security adviser had to resign after falsely denying secret talks with Russia. His White House aides splintered into warring factions. His courtiers gossiped publicly over whose head was next to fall. So what made President Donald Trump angriest when he got out of bed Tuesday morning? Leaks.

“The real story here is why are there so many illegal leaks coming out of Washington?” the president tweeted. “Will these leaks be happening as I deal on N.Korea etc?”

The answer, Mr. President, is yes. The leaks are certain to continue — and thank heaven for that.

The U.S. government is a notoriously leaky collection of institutions. It’s been that way for decades. “The ship of state is the only known vessel that leaks from the top,” James Reston of the New York Times wrote in 1946.

Leaks don’t generally involve secrets that endanger national security. Instead, they fall into two relatively harmless categories: positive leaks to make politicians look wiser than they really are, and negative leaks designed to make rivals look bad. More potent is the whistle-blower leak: the leak that happens when a government official believes something wrong is going on, but can’t find a way to stop it through normal bureaucratic means. That’s what appears to have happened in the case of retired Gen. Michael Flynn.

Flynn talked with the Russian ambassador in December, just after President Barack Obama imposed sanctions on Russia to retaliate for the hacking of U.S. political organizations (including the Hillary Clinton campaign).

David Ignatius of the Washington Post reported on the conversation in mid-January — raising the question of whether Flynn had improperly negotiated over sanctions before Trump’s inauguration. Flynn told Vice President-elect Mike Pence and Trump spokesman Sean Spicer that the sanctions never came up in his talks. Pence and Spicer repeated the denials in public. But that wasn’t true.

On Jan. 26, the Justice Department told Trump’s White House counsel that Flynn’s version was untrue — and that the apparent deception could make him vulnerable to blackmail from Russia. Still, Flynn continued to deny the report.

Then, on Feb. 9, the Post reported that nine current and former officials said Flynn’s version was untrue. On Sunday, the Post added the possibility of Russian blackmail into the mix. On Monday, Flynn resigned.

Two items jump out from that timeline. One is that Trump knew for more than two weeks that Flynn had misled Pence and Spicer but did nothing about it. The second is the unusual number of sources in the Post’s Feb. 9 article: “nine current and former officials who were in senior positions” at the time of Flynn’s phone call. That’s not a leak; that’s an insurrection.

As Trump tries to remake Washington in his own image, it seems he’s going to run into plenty of national security bureaucrats who won’t merely be reluctant to cooperate; they’ll be ready to blow the whistle if the administration does something they consider improper.

That’s far from unprecedented.

In the Watergate scandal that brought down President Richard Nixon, many of the most important leaks came from “Deep Throat,” a source who turned out to be Mark Felt, an associate director of the FBI. His motive, it appears, was to stop Nixon from turning the bureau into a politicized arm of the White House.

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