Washington — When President Vladimir Putin sits down at the table in Helsinki on today, he will surely have in the back of his mind some intelligence worries that have nothing to do with the U.S. president seated across from him.

Putin’s elite spy world has been penetrated by U.S. intelligence. That’s the implication of the extraordinarily detailed 29-page indictment of 12 Russian military intelligence (GRU) officers handed up by special counsel Robert S. Mueller III’s investigators on Friday. The 11-count charge includes names, dates, unit assignments, the GRU’s use of “X-agent” malware, its Bitcoin covert funding schemes and a wealth of other tradecraft.

Putin must be asking himself: How did the Americans find out all these facts? What other operations have been compromised? And how much else do they know?

“The Russians have surely begun a ‘damage assessment’ to figure out how we were able to collect this information and how much damage was done to their cyber capacity as a result,” says Jeffrey Smith, a former CIA general counsel, in an email. “They are probably also doing a CI (counter-intelligence) assessment to determine whether we have any human sources or whether the Russians made mistakes that we were able to exploit.”

Must the GRU assume that officers named in Friday’s indictment are now “blown” for further secret operations? Should Russian spymasters expect that operations they touched are now compromised? What about other Russian operations that used Bitcoin, or X-agent, or another hacking tool called X-Tunnel? Has the U.S. tracked such operations and identified the targets? Finally, how are U.S. intelligence services playing back the information they’ve learned — to recruit, exploit or compromise Russian officers?

“I suspect the senior officers of the GRU who were involved do not have bright futures,” says Smith. “Putin will never extradite them, but it would be great if they were to defect to the U.S. and tell us what they know.”

Looking at this case through a counterintelligence lens raises an intriguing new series of questions. In putting all the detail into the indictment, Mueller was giving Russian intelligence a hint of how much America can see. But this public disclosure may mask much deeper capabilities — perhaps a capacity to expose many more layers of GRU military-intelligence operations and those by the Russian civilian spy services, the FSB and the SVR. U.S. intelligence agencies rarely tip their hand this way by disclosing so much in an indictment; clearly they did so here to send messages.

Explains one former CIA officer: “Given that we clearly had so much of the Russian internal communication and cyber footprints, they must be asking what else do we have? Do we have communications between the units and more senior officers in the GRU? With the General Staff? With the Kremlin? With Putin? Probably not the latter directly, but the Russians are very bureaucratic and it’s hard for me to imagine there is not a clear trail of higher level approvals, progress reports, etc.”

Friday’s indictment is a legal document. But it’s also a shot across the Kremlin’s bow. The message is: If you don’t stop cyber operations against the United States, we have the detailed information to identify and disrupt your intelligence services, officers and sources and methods. Mueller isn’t asking Russia to stop; he’s warning them of the consequences of going forward.

The indictment also sends a message to President Trump and members of his entourage who are potential targets of Mueller’s probe: Here’s a hint of what we know; how much are you willing to wager that we don’t know a lot more about Russian contacts and collusion? For example, the indictment is a proffer of Mueller’s information about contacts between GRU cut-out “Guccifer 2.0” and Roger Stone, Trump’s friend and adviser. What else does Mueller have?

Seeing these details, we have new appreciation for the dilemma of FBI officials James Comey, Peter Strzok and the handful of others who saw the unfolding story of Russia’s secret attempt to undermine Hillary Clinton and help Trump. As Strzok put it in his statement to a House committee Thursday: “In the summer of 2016, I was one of a handful of people who knew the details of Russian election interference and its possible connections with members of the Trump campaign.”

Strzok kept quiet about the conspiracy he was watching. Trump was elected president. But now, at last, with Friday’s indictment, we see a bit of what Strzok and the other intelligence officials saw.

And here’s a spooky final question: How much has the intelligence community told Trump about its operations against Russia? If you were one of the American intelligence officers who helped gather the information that’s included in Friday’s indictment, what would you think about the fact that Trump has asked for a private meeting first with Putin?

— David Ignatius is a columnist for Washington Post Writers Group.