But at the highest levels of government, among those responsible for managing the crisis, the first moment of true foreboding about Russia's intentions arrived with that CIA intelligence.
The material was so sensitive that CIA Director John Brennan kept it out of the President's Daily Brief, concerned that even that restricted report's distribution was too broad. The CIA package came with instructions that it be returned immediately after it was read. To guard against leaks, subsequent meetings in the Situation Room followed the same protocols as planning sessions for the Osama bin Laden raid.
It took time for other parts of the intelligence community to endorse the CIA's view. Only in the administration's final weeks in office did it tell the public, in a declassified report, what officials had learned from Brennan in August - that Putin was working to elect Trump.
Over that five-month interval, the Obama administration secretly debated dozens of options for deterring or punishing Russia, including cyberattacks on Russian infrastructure, the release of CIA-gathered material that might embarrass Putin and sanctions that officials said could "crater" the Russian economy.
But in the end, in late December, Obama approved a modest package combining measures that had been drawn up to punish Russia for other issues - expulsions of 35 diplomats and the closure of two Russian compounds - with economic sanctions so narrowly targeted that even those who helped design them describe their impact as largely symbolic.
Obama also approved a previously undisclosed covert measure that authorized planting cyber weapons in Russia's infrastructure, the digital equivalent of bombs that could be detonated if the United States found itself in an escalating exchange with Moscow. The project, which Obama approved in a covert-action finding, was still in its planning stages when Obama left office. It would be up to President Trump to decide whether to use the capability.
In political terms, Russia's interference was the crime of the century, an unprecedented and largely successful destabilizing attack on American democracy. It was a case that took almost no time to solve, traced to the Kremlin through cyber-forensics and intelligence on Putin's involvement. And yet, because of the divergent ways Obama and Trump have handled the matter, Moscow appears unlikely to face proportionate consequences.
Those closest to Obama defend the administration's response to Russia's meddling. They note that by August it was too late to prevent the transfer to WikiLeaks and other groups of the troves of emails that would spill out in the ensuing months. They believe that a series of warnings - including one that Obama delivered to Putin in September - prompted Moscow to abandon any plans of further aggression, such as sabotage of U.S. voting systems.
Denis McDonough, who served as Obama's chief of staff, said that the administration regarded Russia's interference as an attack on the "heart of our system."
"We set out from a first-order principle that required us to defend the integrity of the vote," McDonough said in an interview. "Importantly, we did that. It's also important to establish what happened and what they attempted to do so as to ensure that we take the steps necessary to stop it from happening again."
But other administration officials look back on the Russia period with remorse.
"It is the hardest thing about my entire time in government to defend," said a former senior Obama administration official involved in White House deliberations on Russia. "I feel like we sort of choked."
The post-election period has been dominated by the overlapping investigations into whether Trump associates colluded with Russia before the election and whether the president sought to obstruct the FBI probe afterward. That spectacle has obscured the magnitude of Moscow's attempt to hijack a precious and now vulnerable-seeming American democratic process.
Beset by allegations of hidden ties between his campaign and Russia, Trump has shown no inclination to revisit the matter and has denied any collusion or obstruction on his part. As a result, the expulsions and modest sanctions announced by Obama on Dec. 29 continue to stand as the United States' most forceful response.
"The punishment did not fit the crime," said Michael McFaul, who served as U.S. ambassador to Russia for the Obama administration from 2012 to 2014. "Russia violated our sovereignty, meddling in one of our most sacred acts as a democracy - electing our president. The Kremlin should have paid a much higher price for that attack. And U.S. policymakers now - both in the White House and Congress - should consider new actions to deter future Russian interventions."
The Senate this month passed a bill that would impose additional election- and Ukraine-related sanctions on Moscow and limit Trump's ability to lift them. The measure requires House approval, however, and Trump's signature.
This account of the Obama administration's response to Russia's interference is based on interviews with more than three dozen current and former U.S. officials in senior positions in government, including at the White House, the State, Defense and Homeland Security departments, and U.S. intelligence services. Most agreed to speak only on the condition of anonymity, citing the sensitivity of the issue.
The White House, the CIA, the FBI, the National Security Agency and the Office of the Director of National Intelligence declined to comment.
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The CIA breakthrough came at a stage of the presidential campaign when Trump had secured the GOP nomination but was still regarded as a distant long shot. Clinton held comfortable leads in major polls, and Obama expected that he would be transferring power to someone who had served in his Cabinet.
The intelligence on Putin was extraordinary on multiple levels, including as a feat of espionage.
For spy agencies, gaining insights into the intentions of foreign leaders is among the highest priorities. But Putin is a remarkably elusive target. A former KGB officer, he takes extreme precautions to guard against surveillance, rarely communicating by phone or computer, always running sensitive state business from deep within the confines of the Kremlin.
The Washington Post is withholding some details of the intelligence at the request of the U.S. government.
In early August, Brennan alerted senior White House officials to the Putin intelligence, making a call to deputy national security adviser Avril Haines and pulling national security adviser Susan E. Rice aside after a meeting before briefing Obama along with Rice, Haines and McDonough in the Oval Office.
Officials described the president's reaction as grave. Obama "was deeply concerned and wanted as much information as fast as possible," a former official said. "He wanted the entire intelligence community all over this."
Concerns about Russian interference had gathered throughout the summer.
Russia experts had begun to see a troubling pattern of propaganda in which fictitious news stories, assumed to be generated by Moscow, proliferated across social-media platforms.
Officials at the State Department and FBI became alarmed by an unusual spike in requests from Russia for temporary visas for officials with technical skills seeking permission to enter the United States for short-term assignments at Russian facilities. At the FBI's behest, the State Department delayed approving the visas until after the election.
Meanwhile, the FBI was tracking a flurry of hacking activity against U.S. political parties, think tanks and other targets. Russia had gained entry to DNC systems in the summer of 2015 and spring of 2016, but the breaches did not become public until they were disclosed in a June 2016 report by The Post.
Even after the late-July WikiLeaks dump, which came on the eve of the Democratic convention and led to the resignation of Rep. Debbie Wasserman Schultz, D-Fla., as the DNC's chairwoman, U.S. intelligence officials continued to express uncertainty about who was behind the hacks or why they were carried out.
At a public security conference in Aspen, Colo., in late July, Director of National Intelligence James Clapper noted that Russia had a long history of meddling in American elections but that U.S. spy agencies were not ready to "make the call on attribution" for what was happening in 2016.
"We don't know enough . . . to ascribe motivation," Clapper said. "Was this just to stir up trouble or was this ultimately to try to influence an election?"
The August intelligence on Putin obtained by the CIA seemed to fill some of those critical gaps.
Brennan convened a secret task force at CIA headquarters composed of several dozen analysts and officers from the CIA, the NSA and the FBI.
The unit functioned as a sealed compartment, its work hidden from the rest of the intelligence community. Those brought in signed new non-disclosure agreements to be granted access to intelligence from all three participating agencies.
They worked exclusively for two groups of "customers," officials said. The first was Obama and fewer than 14 senior officials in government. The second was a team of operations specialists at the CIA, NSA and FBI who took direction from the task force on where to aim their subsequent efforts to collect more intelligence on Russia.
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The secrecy extended into the White House.
Rice, Haines and White House homeland-security adviser Lisa Monaco convened meetings in the Situation Room to weigh the mounting evidence of Russian interference and generate options for how to respond. At first, only four senior security officials were allowed to attend: Brennan, Clapper, Attorney General Loretta Lynch and FBI Director James Comey. Aides ordinarily allowed entry as "plus-ones" were barred.
Gradually, the circle widened to include Vice President Joe Biden and others. Agendas sent to Cabinet secretaries - including John Kerry at the State Department and Ashton Carter at the Pentagon - arrived in envelopes that subordinates were not supposed to open. Sometimes the agendas were withheld until participants had taken their seats in the Situation Room.
Throughout his presidency, Obama's approach to national security challenges was deliberate and cautious. He came into office seeking to end wars in Iraq and Afghanistan. He was loath to act without support from allies overseas and firm political footing at home. He was drawn only reluctantly into foreign crises, such as the civil war in Syria, that presented no clear exit for the United States.
Obama's approach often seemed reducible to a single imperative: Don't make things worse. As brazen as the Russian attacks on the election seemed, Obama and his top advisers feared that things could get far worse.
They were concerned that any pre-election response could provoke an escalation from Putin. Moscow's meddling to that point was seen as deeply concerning but unlikely to materially affect the outcome of the election. Far more worrisome to the Obama team was the prospect of a cyber-assault on voting systems before and on Election Day.
They also worried that any action they took would be perceived as political interference in an already volatile campaign. By August, Trump was predicting that the election would be rigged. Obama officials feared providing fuel to such claims, playing into Russia's efforts to discredit the outcome and potentially contaminating the expected Clinton triumph.
Before departing for an August vacation to Martha's Vineyard, Obama instructed aides to pursue ways to deter Moscow and proceed along three main paths: Get a high-confidence assessment from U.S. intelligence agencies on Russia's role and intent; shore up any vulnerabilities in state-run election systems; and seek bipartisan support from congressional leaders for a statement condemning Moscow and urging states to accept federal help.
The administration encountered obstacles at every turn.
Despite the intelligence the CIA had produced, other agencies were slower to endorse a conclusion that Putin was personally directing the operation and wanted to help Trump. "It was definitely compelling, but it was not definitive," said one senior administration official. "We needed more."
Some of the most critical technical intelligence on Russia came from another country, officials said. Because of the source of the material, the NSA was reluctant to view it with high confidence.
Brennan moved swiftly to schedule private briefings with congressional leaders. But getting appointments with certain Republicans proved difficult, officials said, and it was not until after Labor Day that Brennan had reached all members of the "Gang of Eight" - the majority and minority leaders of both houses and the chairmen and ranking Democrats on the Senate and House intelligence committees.
Jeh Johnson, the homeland-security secretary, was responsible for finding out whether the government could quickly shore up the security of the nation's archaic patchwork of voting systems. He floated the idea of designating state mechanisms "critical infrastructure," a label that would have entitled states to receive priority in federal cybersecurity assistance, putting them on a par with U.S. defense contractors and financial networks.
On Aug. 15, Johnson arranged a conference call with dozens of state officials, hoping to enlist their support. He ran into a wall of resistance.
The reaction "ranged from neutral to negative," Johnson said in congressional testimony Wednesday.
Brian Kemp, the Republican secretary of state of Georgia, used the call to denounce Johnson's proposal as an assault on state rights. "I think it was a politically calculated move by the previous administration," Kemp said in a recent interview, adding that he remains unconvinced that Russia waged a campaign to disrupt the 2016 race. "I don't necessarily believe that," he said.
Stung by the reaction, the White House turned to Congress for help, hoping that a bipartisan appeal to states would be more effective.
In early September, Johnson, Comey and Monaco arrived on Capitol Hill in a caravan of black SUVs for a meeting with 12 key members of Congress, including the leadership of both parties.
The meeting devolved into a partisan squabble.
"The Dems were, 'Hey, we have to tell the public,' " recalled one participant. But Republicans resisted, arguing that to warn the public that the election was under attack would further Russia's aim of sapping confidence in the system.
Senate Majority Leader Mitch McConnell, R-Ky., went further, officials said, voicing skepticism that the underlying intelligence truly supported the White House's claims. Through a spokeswoman, McConnell declined to comment, citing the secrecy of that meeting.
Key Democrats were stunned by the GOP response and exasperated that the White House seemed willing to let Republican opposition block any pre-election move.
On Sept. 22, two California Democrats - Sen. Dianne Feinstein and Rep. Adam Schiff - did what they couldn't get the White House to do. They issued a statement making clear that they had learned from intelligence briefings that Russia was directing a campaign to undermine the election, but they stopped short of saying to what end.
A week later, McConnell and other congressional leaders issued a cautious statement that encouraged state election officials to ensure their networks were "secure from attack." The release made no mention of Russia and emphasized that the lawmakers "would oppose any effort by the federal government" to encroach on the states' authorities.
When U.S. spy agencies reached unanimous agreement in late September that the interference was a Russian operation directed by Putin, Obama directed spy chiefs to prepare a public statement summarizing the intelligence in broad strokes.
With Obama still determined to avoid any appearance of politics, the statement would not carry his signature.
On Oct. 7, the administration offered its first public comment on Russia's "active measures," in a three-paragraph statement issued by Johnson and Clapper. Comey had initially agreed to attach his name, as well, officials said, but changed his mind at the last minute, saying that it was too close to the election for the bureau to be involved.
"The U.S. intelligence community is confident that the Russian government directed the recent compromises of emails from U.S. persons and institutions, including from U.S. political organizations," the statement said. "We believe, based on the scope and sensitivity of these efforts, that only Russia's senior-most officials could have authorized these activities."
Early drafts accused Putin by name, but the reference was removed out of concern that it might endanger intelligence sources and methods.
The statement was issued around 3:30 p.m., timed for maximum media coverage. Instead, it was quickly drowned out. At 4 p.m., The Post published a story about crude comments Trump had made about women that were captured on an "Access Hollywood" tape. Half an hour later, WikiLeaks published its first batch of emails stolen from Clinton campaign chairman John Podesta.
To some, Obama's determination to avoid politicizing the Russia issue had the opposite effect: It meant that he allowed politics to shape his administration's response to what some believed should have been treated purely as a national security threat.
Schiff said that the administration's justifications for inaction often left him with a sense of "cognitive dissonance."
"The administration doesn't need congressional support to issue a statement of attribution or impose sanctions," Schiff said in a recent interview. He said many groups inadvertently abetted Russia's campaign, including Republicans who refused to confront Moscow and media organizations that eagerly mined the troves of hacked emails.
"Where Democrats need to take responsibility," Schiff said, "is that we failed to persuade the country why they should care that a foreign power is meddling in our affairs."
The Situation Room is actually a complex of secure spaces in the basement level of the West Wing. A video feed from the main room courses through some National Security Council offices, allowing senior aides sitting at their desks to see - but not hear - when meetings are underway.
As the Russia-related sessions with Cabinet members began in August, the video feed was shut off. The last time that had happened on a sustained basis, officials said, was in the spring of 2011 during the run-up to the U.S. Special Operations raid on bin Laden's compound in Pakistan.
The blacked-out screens were seen as an ominous sign among lower-level White House officials who were largely kept in the dark about the Russia deliberations even as they were tasked with generating options for retaliation against Moscow.
Much of that work was led by the Cyber Response Group, an NSC unit with representatives from the CIA, NSA, State Department and Pentagon.
The early options they discussed were ambitious. They looked at sectorwide economic sanctions and cyberattacks that would take Russian networks temporarily offline. One official informally suggested - though never formally proposed - moving a U.S. naval carrier group into the Baltic Sea as a symbol of resolve.
What those lower-level officials did not know was that the principals and their deputies had by late September all but ruled out any pre-election retaliation against Moscow. They feared that any action would be seen as political and that Putin, motivated by a seething resentment of Clinton, was prepared to go beyond fake news and email dumps.
The FBI had detected suspected Russian attempts to penetrate election systems in 21 states, and at least one senior White House official assumed that Moscow would try all 50, officials said. Some officials believed the attempts were meant to be detected to unnerve the Americans. The patchwork nature of the United States' 3,000 or so voting jurisdictions would make it hard for Russia to swing the outcome, but Moscow could still sow chaos.
"We turned to other scenarios" the Russians might attempt, said Michael Daniel, who was cybersecurity coordinator at the White House, "such as disrupting the voter rolls, deleting every 10th voter [from registries] or flipping two digits in everybody's address."
The White House also worried that they had not yet seen the worst of Russia's campaign. WikiLeaks and DCLeaks, a website set up in June 2016 by hackers believed to be Russian operatives, already had troves of emails. But U.S. officials feared that Russia had more explosive material or was willing to fabricate it.
"Our primary interest in August, September and October was to prevent them from doing the max they could do," said a senior administration official. "We made the judgment that we had ample time after the election, regardless of outcome, for punitive measures."
The assumption that Clinton would win contributed to the lack of urgency.
Instead, the administration issued a series of warnings.
Brennan delivered the first on Aug. 4 in a blunt phone call with Alexander Bortnikov, the director of the FSB, Russia's powerful security service.
A month later, Obama confronted Putin directly during a meeting of world leaders in Hangzhou, China. Accompanied only by interpreters, Obama told Putin that "we knew what he was doing and [he] better stop or else," according to a senior aide who subsequently spoke with Obama. Putin responded by demanding proof and accusing the United States of interfering in Russia's internal affairs.
In a subsequent news conference, Obama alluded to the exchange and issued a veiled threat. "We're moving into a new era here where a number of countries have significant capacities," he said. "Frankly, we've got more capacity than anybody both offensively and defensively."
There were at least two other warnings.
On Oct. 7, the day that the Clapper-Johnson statement was released, Rice summoned Russian Ambassador Sergey Kislyak to the White House and handed him a message to relay to Putin.
Then, on Oct. 31, the administration delivered a final pre-election message via a secure channel to Moscow originally created to avert a nuclear exchange. The message noted that the United States had detected malicious activity, originating from servers in Russia, targeting U.S. election systems and warned that meddling would be regarded as unacceptable interference. Russia confirmed the next day that it had received the message but replied only after the election through the same channel, denying the accusation.
As Election Day approached, proponents of taking action against Russia made final, futile appeals to Obama's top aides: McDonough, Rice and Haines. Because their offices were part of a suite of spaces in the West Wing, securing their support on any national security issue came to be known as "moving the suite."
One of the last to try before the election was Kerry. Often perceived as reluctant to confront Russia, in part to preserve his attempts to negotiate a Syria peace deal, Kerry was at critical moments one of the leading hawks.
In October, Kerry's top aides had produced an "action memo" that included a package of retaliatory measures including economic sanctions. Knowing the White House was not willing to act before the election, the plan called for the measures to be announced almost immediately after votes had been securely cast and counted.
Kerry signed the memo and urged the White House to convene a principals meeting to discuss the plan, officials said. "The response was basically, 'Not now,' " one official said.
Election Day arrived without penalty for Moscow.
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Despite the dire warnings, there were no meltdowns in the United States' voting infrastructure on Nov. 8, no evidence of hacking-related fraud, crashing of electronic ballots or manipulation of vote counts.
The outcome itself, however, was a shock.
Suddenly, Obama faced a successor who had praised WikiLeaks and prodded Moscow to steal even more Clinton emails, while dismissing the idea that Russia was any more responsible for the election assault than "somebody sitting on their bed that weighs 400 pounds."
"The White House was mortified and shocked," said a former administration official. "From national security people there was a sense of immediate introspection, of, 'Wow, did we mishandle this.' "
At first, there was no outward sign of new resolve.
After his failed pre-election bid, Kerry returned with a fallback proposal, calling for the creation of a bipartisan commission to investigate Russian interference and make recommendations on how to protect future elections.
The panel would be modeled on the commission that investigated the Sept. 11, 2001, attacks, producing a definitive report and making recommendations that led to the overhaul of U.S. intelligence agencies.
"The idea was that if you think doing something aggressive is too inflammatory, then we shouldn't have a problem getting to the truth about what happened," said an administration official familiar with the Kerry plan. Trump was expected to oppose such a plan, but setting it in motion before he was sworn in would make it "harder and uglier politically" for him to block.
Supporters' confidence was buoyed when McDonough signaled that he planned to "tabledrop" the proposal at the next NSC meeting, one that would be chaired by Obama. Kerry was overseas and participated by videoconference.
To some, the "tabledrop" term has a tactical connotation beyond the obvious. It is sometimes used as a means of securing approval of an idea by introducing it before opponents have a chance to form counterarguments.
"We thought this was a good sign," a former State Department official said.
But as soon as McDonough introduced the proposal for a commission, he began criticizing it, arguing that it would be perceived as partisan and almost certainly blocked by Congress.
Obama then echoed McDonough's critique, effectively killing any chance that a Russia commission would be formed.
McDonough declined to comment on the principals' committee meeting on the commission or any other sensitive matters but acknowledged that he opposed the idea, in part because he believed it would be premature to do so before U.S. intelligence agencies and Congress had conducted their investigations.
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Several officials described the post-election atmosphere at the White House as somber. "It was like a funeral parlor," according to one official who said that work on Russia and other subjects slowed as officials began to anticipate the damage to Obama's policies and legacy.
Others disputed that characterization, saying that the NSC carried on with no interruption or diminution of focus. "Nobody got paralyzed by grief," a high-ranking official said. "We all did our jobs."
Rice declined to comment on White House deliberations or other sensitive matters but said that the administration always planned to respond to Russia, regardless of the outcome of the election. "We felt it was on our watch and that we had to do something about it. It was our responsibility," Rice said.
Whatever the case, work on Russia did not resume in earnest until after Thanksgiving, in part because Obama made his last foreign trip.
Rice again ordered NSC staffers to finalize a "menu" of punitive measures to use against Moscow. The list that took shape was a distillation of ideas that had been circulating for months across three main categories: cyber, economic and diplomatic.
Again, the discussion ran into roadblocks.
Spy agencies wanted to maintain their penetrations of Russian networks, not expose them in a cyber-fusillade.
Treasury Department officials devised plans that would hit entire sectors of Russia's economy. One preliminary suggestion called for targeting technology companies including Kaspersky Lab, the Moscow-based cybersecurity firm. But skeptics worried that the harm could spill into Europe and pointed out that U.S. companies used Kaspersky systems and software.
Several senior administration officials called for imposing sanctions on Putin personally or releasing financial records or other information that would embarrass him. Some objected that the latter proposal would send the wrong message - the United States would be engaging in the same behavior it was condemning. In any case, it was not clear how long it would take U.S. spy agencies to assemble such a Putin dossier.
"By December, those of us working on this for a long time were demoralized," said an administration official involved in the developing punitive options.
Then the tenor began to shift.
On Dec. 9, Obama ordered a comprehensive review by U.S. intelligence agencies of Russian interference in U.S. elections going back to 2008, with a plan to make some of the findings public.
A week later, in one of Obama's final news briefings, he expressed irritation that such a consequential election "came to be dominated by a bunch of these leaks." He scolded news organizations for an "obsession" with titillating material about the Democrats that had dominated coverage.
Then he unloaded on Moscow. "The Russians can't change us or significantly weaken us," he said. "They are a smaller country. They are a weaker country. Their economy doesn't produce anything that anybody wants to buy, except oil and gas and arms."
It was a rare outburst for Obama, one that came amid a wave of internal second-guessing, finger-pointing from members of the defeated Clinton campaign, and the post-election posturing of Putin and Trump.
There was another factor at work, however.
Obama's decision to order a comprehensive report on Moscow's interference from U.S. spy agencies had prompted analysts to go back through their agencies' files, scouring for previously overlooked clues.
The effort led to a flurry of new, disturbing reports - many of them presented in the President's Daily Brief - about Russia's subversion of the 2016 race. The emerging picture enabled policymakers to begin seeing the Russian campaign in broader terms, as a comprehensive plot sweeping in its scope.
Ben Rhodes, former deputy national security adviser, said that the DNC email penetrations were initially thought to be in the same vein as previous Russian hacking efforts against targets including the State Department and White House.
"In many ways . . . we dealt with this as a cyberthreat and focused on protecting our cyber infrastructure," Rhodes said in an interview. "Meanwhile, the Russians were playing this much bigger game, which included elements like released hacked materials, political propaganda and propagating fake news, which they'd pursued in other countries."
"We weren't able to put all of those pieces together in real time," Rhodes said, "and in many ways that complete picture is still being filled in." Rhodes declined to discuss any sensitive information.
Obama's darkened mood, the intelligence findings and the approaching transfer of power gave new urgency to NSC deliberations. In mid-December, as Cabinet members took turns citing drawbacks to various proposals for retaliating against Russia, Rice grew impatient and began cutting them off.
"We're not talking anymore. We're acting," she said, according to one participant.
Rice moved swiftly through a list of proposals that had survived months of debate, a menu that allowed principals to vote for what one participant described as "heavy, medium and light" options.
Among those in the Situation Room were Clapper, Brennan, Kerry and Deputy FBI Director Andrew McCabe. Rice challenged them go to the "max of their comfort zones," a second participant said.
Economic sanctions, originally aimed only at Russia's military intelligence service, were expanded to include the FSB, a domestic successor to the KGB. Four Russian intelligence officials and three companies with links to those services were also named as targets.
The FBI had long lobbied to close two Russian compounds in the United States - one in Maryland and another in New York - on the grounds that both were used for espionage and placed an enormous surveillance burden on the bureau.
The FBI was also responsible for generating the list of Russian operatives working under diplomatic cover to expel, drawn from a roster the bureau maintains of suspected Russian intelligence agents in the United States.
Cabinet officials were prompted to vote on whether to close one Russian compound or two, whether to kick out around 10 suspected Russian agents, 20 or 35.
Kerry laid out his department's concerns. The U.S. ambassador to Russia, John Tefft, had sent a cable warning that Moscow would inevitably expel the same number of Americans from Moscow and that departures of that magnitude would impair the embassy's ability to function.
The objections were dismissed, and Rice submitted a plan to Obama calling for the seizure of both Russian facilities and the expulsion of 35 suspected spies. Obama signed off on the package and announced the punitive measures on Dec. 29, while on vacation in Hawaii.
By then, the still-forming Trump administration was becoming entangled by questions about contacts with Moscow. On or around that same day that Obama imposed sanctions, Trump's designated national security adviser, retired Lt. Gen. Michael Flynn, told the Russian ambassador by phone that the sanctions would soon be revisited. Flynn's false statements about that conversation later cost him his job.
The report that Obama had commissioned was released a week later, on Jan. 6. It was based largely on the work done by the task force Brennan had established and made public what the CIA had concluded in August, that "Putin and the Russian government aspired to help President-elect Trump's election chances when possible by discrediting Secretary Clinton."
It also carried a note of warning: "We assess Moscow will apply lessons learned from its Putin-ordered campaign aimed at the U.S. election to future influence efforts worldwide."
The punitive measures got several days of media attention before the spotlight returned to Trump, his still-forming administration and, later, the initial rumblings of the Russia crisis that has become a consuming issue for the Trump White House.
But the package of measures approved by Obama, and the process by which they were selected and implemented, were more complex than initially understood.
The expulsions and compound seizures were originally devised as ways to retaliate against Moscow not for election interference but for an escalating campaign of harassment of American diplomats and intelligence operatives. U.S. officials often endured hostile treatment, but the episodes had become increasingly menacing and violent.
In one previously undisclosed incident on July 6, a Russian military helicopter dropped from the sky to make multiple passes just feet over the hood of a vehicle being driven by the U.S. defense attache, who was accompanied by colleagues, on a stretch of road between Murmansk and Pechenga in northern Russia. The attempt at intimidation was captured on photos the Americans took through the windshield.
An even more harrowing encounter took place the prior month, when a CIA operative returning by taxi to the U.S. Embassy in Moscow was tackled and thrown to the ground by a uniformed FSB guard. In a video aired on Russian television, the U.S. operative can be seen struggling to drag himself across the embassy threshold and onto U.S. sovereign territory. He sustained a broken shoulder in the attack.
Though conceived as retaliation for those incidents, the expulsions were adapted and included in the election-related package. The roster of expelled spies included several operatives who were suspected of playing a role in Russia's election interference from within the United States, officials said. They declined to elaborate.
More broadly, the list of 35 names focused heavily on Russians known to have technical skills. Their names and bios were laid out on a dossier delivered to senior White House officials and Cabinet secretaries, although the list was modified at the last minute to reduce the number of expulsions from Russia's U.N. mission in New York and add more names from its facilities in Washington and San Francisco.
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The compounds were even higher on the FBI's wish list.
At one point in the White House deliberations, intelligence analysts used aerial images of the facilities to show how they had been modified to enhance their espionage capabilities. Slides displayed in the Situation Room showed new chimneys and other features, all presumed to allow for the installation of more-sophisticated eavesdropping equipment aimed at U.S. naval facilities and the NSA headquarters at Fort Meade in Maryland.
Rice pointed to the FBI's McCabe and said: "You guys have been begging to do this for years. Now is your chance."
The administration gave Russia 24 hours to evacuate the sites, and FBI agents watched as fleets of trucks loaded with cargo passed through the compounds' gates.
When FBI agents entered the sites, they found them stripped of antennas, electronics, computers, file cabinets and other gear, officials said, their hasty removal leaving visible markings on floors, tables and walls.
Economic sanctions are widely seen as the United States' most potent lever, short of military force. Russia's economy is dwarfed by that of the United States, and nearly every major Russian institution and oligarch depends to some degree on access to U.S. and Western financial institutions, networks and credit.
Sanctions that the United States and Europe imposed on Russia in 2014 for its actions in Ukraine were damaging. Coinciding with a sharp drop in oil prices, those measures contributed to a 4 percent contraction in the Russian economy and sent its reserves plunging.
The election-related sanctions, by contrast, have had no such impact.
Officials involved in designing them said that the main targets - Russia's foreign and military intelligence services, the GRU and FSB, and senior officials at those agencies - have few known holdings abroad or vulnerable assets to freeze.
"I don't think any of us thought of sanctions as being a primary way of expressing our disapproval" for the election interference, said a senior administration official involved in the decision. "Going after their intelligence services was not about economic impact. It was symbolic."
More than any other measure, that decision has become a source of regret to senior administration officials directly involved in the Russia debate. The outcome has left the impression that Obama saw Russia's military meddling in Ukraine as more deserving of severe punishment than its subversion of a U.S. presidential race.
"What is the greater threat to our system of government?" said a former high-ranking administration official, noting that Obama and his advisers knew from projections formulated by the Treasury Department that the impact of the election-related economic sanctions would be "minimal."
The most difficult measure to evaluate is one that Obama alluded to in only the most oblique fashion when announcing the U.S. response.
"We will continue to take a variety of actions at a time and place of our choosing, some of which will not be publicized," he said in a statement released by the White House.
He was referring, in part, to a cyber operation that was designed to be detected by Moscow but not cause significant damage, officials said. The operation, which entailed implanting computer code in sensitive computer systems that Russia was bound to find, served only as a reminder to Moscow of the United States' cyber reach.
But Obama also signed the secret finding, officials said, authorizing a new covert program involving the NSA, CIA and U.S. Cyber Command.
Obama declined to comment for this article, but a spokesman issued a statement: "This situation was taken extremely seriously, as is evident by President Obama raising this issue directly with President Putin; 17 intelligence agencies issuing an extraordinary public statement; our homeland security officials working relentlessly to bolster the cyber defenses of voting infrastructure around the country; the President directing a comprehensive intelligence review, and ultimately issuing a robust response including shutting down two Russian compounds, sanctioning nine Russian entities and individuals, and ejecting 35 Russian diplomats from the country."
The cyber operation is still in its early stages and involves deploying "implants" in Russian networks deemed "important to the adversary and that would cause them pain and discomfort if they were disrupted," a former U.S. official said.
The implants were developed by the NSA and designed so that they could be triggered remotely as part of retaliatory cyber-strike in the face of Russian aggression, whether an attack on a power grid or interference in a future presidential race.
Officials familiar with the measures said that there was concern among some in the administration that the damage caused by the implants could be difficult to contain.
As a result, the administration requested a legal review, which concluded that the devices could be controlled well enough that their deployment would be considered "proportional" in varying scenarios of Russian provocation, a requirement under international law.
The operation was described as long-term, taking months to position the implants and requiring maintenance thereafter. Under the rules of covert action, Obama's signature was all that was necessary to set the operation in motion.
U.S. intelligence agencies do not need further approval from Trump, and officials said that he would have to issue a countermanding order to stop it. The officials said that they have seen no indication that Trump has done so.
