Former National Security Adviser Lt. General Michael Flynn's Friday guilty plea to making false statements to the FBI about his conversations before President Donald Trump’s inauguration— reportedly a deal in exchange for his cooperation with the investigation of retired FBI director Robert Mueller — is bad news for Trump.

It shouldn't be surprisingly bad news: After all, Trump didn’t allegedly pressure former FBI director James Comey to drop the investigation into Flynn, nor then fire Comey when he refused because he thought that Flynn hadn’t done anything that would implicate Trump and/or his close associates.

But it shows that Mueller is leading a serious, meticulous investigation that is carefully being built from the ground up, like an organized crime investigation, which won’t be easy for Trump to derail. Flynn would not have been offered a plea on a relatively minor charge if Mueller didn’t think he had information that was valuable to his investigation.

The facts to which Flynn agreed in his plea are in themselves very damning to Trump: Most critically, Flynn has acknowledged that at least one his conversations with Kislyak took place at the direction of a “very senior” official on Trump’s transition team — reportedly,Trump’s son-in-law Jared Kushner — who asked Flynn to ask Kislyak to oppose or delay a United Nations Security Council resolution declaring Israeli settlements in the West Bank illegal.

So not only is Kushner also now in substantial legal jeopardy, but this latest revelation brings the personal ties between the Trump campaign and the Russian government not only into Trump’s closest political circles, but into his family.

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Worse yet is, according to a report from ABC News, that Flynn is prepared to testify that Trump asked him to speak with representatives of the Russian government during the campaign. That would suggest significant ties between the campaign and a state that was almost certainly intervening in the election in favor of Trump.

Flynn would not have been offered a plea on a relatively minor charge if Mueller didn’t think he had information that was valuable.

Still, it’s impossible to know at this point precisely where Mueller’s investigation will lead. Flynn may well have information that is seriously damaging for senior advisers besides Kushner — like Donald Trump Jr. who, during the campaign, met with a Russian lawyer who claimed to have information from the Russian government that was damaging to Hillary Clinton.

But everyone implicated by Flynn would become someone else with incentives to provide further information. It’s entirely possible that this chain of testimony could lead all the way to the president himself; at a minimum, some of his closest advisers are very likely to be implicated

This doesn’t guarantee, of course, that Flynn or any other Trump associate will end up in jail or that Mueller’s investigation will fully play out. Trump has two formidable weapons he can still use. The first is a plenary power to pardon people for federal offenses, including preemptively. If the investigation gets too close, Trump could simply pardon Flynn, Kushner, his sons and anyone else Mueller’s investigation might implicate.

Because of the care Mueller is evidently taking with his investigation, however, Trump might not be able to escape trouble so easily.

And, should Mueller’s investigation continue to accumulate damning information, Trump could also have it shut down. If Deputy Attorney General Rod Rosenstein — who is ultimately in charge of the Mueller investigation because Attorney General Jeff Sessions recused himself over his own meetings with Russian officials — refused to shut down Mueller’s investigation, Trump could fire him and find someone in the Justice Department who would.

Because of the care Mueller is evidently taking with his investigation, however, Trump might not be able to escape trouble so easily. Trump’s pardon power doesn’t extend to state crimes, and Mueller’s investigation may well uncover illegal activity (including money laundering) that is illegal under New York as well as federal law. Were Trump to shut down Mueller’s federal investigation, New York Attorney General Eric Schneiderman would likely be particularly inclined to be aggressive in investigating violations of state law by Trump and his associates — and Mueller is certainly aware of this.

Still, if Trump issues blanket pardons or terminates Mueller’s investigation, the short-term remedies at the federal level might be limited. It is clear that Senate Majority Leader Mitch McConnell and Speaker of the House Paul Ryan will not seriously investigate Trump, let alone impeach and convict him, as long as he will advance their agenda.

Ultimately, payback for Trump’s actions may have to be at the ballot box next November, and then in 2020.

Scott Lemieux is a lecturer in the Department of Political Science at the University of Washington. He is the co-author of Judicial Review and Democratic Theory and contributes regularly to The Week, Reuters and the New Republic.