Obama Confronts Complexity of Using a Mighty Cyberarsenal Against Russia

WASHINGTON — Over the past four months, American intelligence agencies and aides to President Obama assembled a menu of options to respond to Russia’s hacking during the election, ranging from the obvious — exposing President Vladimir V. Putin’s financial ties to oligarchs — to the innovative, including manipulating the computer code that Russia uses in designing its cyberweapons.

But while Mr. Obama vowed on Friday to “send a clear message to Russia” as both a punishment and a deterrent, some of the options were rejected as ineffective, others as too risky. If the choices had been better, one of the aides involved in the debate noted recently, the president would have acted by now.

In his last weeks in office, that Situation Room debate has confronted a naturally cautious president with a complex calculus that President-elect Donald J. Trump will soon inherit: how to use the world’s most powerful cyberarsenal at a moment when the United States, as the election showed, remains highly vulnerable.

“Is there something we can do to them, that they would see, they would realize 98 percent that we did it, but that wouldn’t be so obvious that they would then have to respond for their own honor?” David H. Petraeus, the former director of the Central Intelligence Agency under Mr. Obama, asked on Friday, at a conference here sponsored by Harvard’s Belfer Center for Science and International Affairs. “The question is how subtle do you want it, how damaging do you want it, how do you try to end it here rather than just ratchet it up?”

The idea of exposing Mr. Putin’s links to oligarchs was set aside after some aides argued that it would not come as a shock to Russians. Still, there are proposals to cut off leaders in Mr. Putin’s inner circle from their hidden bank accounts in Europe and Asia. There is an option to use sanctions under a year-old executive order to ban international travel for senior officials in the G.R.U., the Russian military intelligence unit that American spy agencies say stole emails from the Democratic National Committee and Hillary Clinton’s campaign chairman, then doled them out to WikiLeaks, betting that media outlets eager for insider details would amplify them, doing the Kremlin’s work for it.

The National Security Agency and its military cousin, the United States Cyber Command, which is responsible for computer-network warfare, have worked up other ideas, officials said, though some have been rejected by the Pentagon.

Those plans could deploy the world-class arsenal of cyberweapons assembled at a cost of billions of dollars during Mr. Obama’s tenure to expose or neutralize some of the hacking tools favored by Russia’s spies — the digital equivalent of a pre-emptive strike. But the selection of targets by Americans and the accuracy of that retaliation could also expose software “implants” that the United States has patiently inserted and nurtured in Russian networks, in case of future cyberconflicts.

And the revelation in August about some of the N.S.A.’s own tools for breaking into foreign computer networks has raised the possibility that the Russians are already inside American networks and are sending a warning that they can respond in kind.

All of this has led Mr. Obama to ask how the Russians might escalate the confrontation, and whether the United States in the end may have more to lose than Russia.

“He doesn’t have great options,” said Michael D. McFaul, formerly one of Mr. Obama’s top national security aides and then his ambassador to Moscow.

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