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WASHINGTON — With rebel forces in Syria in retreat and the Obama administration’s policy toward the war-ravaged country in disarray, Secretary of State John Kerry arrived at the White House Situation Room one day in June with a document bearing a warning. President Bashar al-Assad of Syria had used chemical weapons against his people, the document said, and if the United States did not “impose consequences,” Mr. Assad would see it as a “green light for continued CW use.”









President Obama had signed a secret order in April — months earlier than previously reported — authorizing a C.I.A. plan to begin arming the Syrian rebels. But the arms had not been shipped, and the collapse of rebel positions in western Syria fueled the atmosphere of crisis that hung over the June meeting.

Yet after hours of debate in which top advisers considered a range of options, including military strikes and increased support to the rebels, the meeting ended the way so many attempts to define a Syrian strategy had ended in the past, with the president’s aides deeply divided over how to respond to a civil war that had already claimed 100,000 lives.

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The State Department’s June warning, laid out in a document obtained by The New York Times, proved to be prophetic. A devastating poison gas attack on Aug. 21 killed hundreds of civilians, touching off a crisis that brought the United States close to launching military strikes in Syria and that ended only when Mr. Obama seized on a Russian-sponsored agreement to secure Syria’s chemical weapons.

Now, two years after Mr. Obama publicly declared that Mr. Assad had to go, he is banking on the success of that Russian-initiated plan — which relies on Mr. Assad’s cooperation and which the Syrian president offered in a recent interview as a convenient shield against American intervention.

But as Mr. Kerry held meetings in London with representatives of Syrian opposition groups on Tuesday in the hopes of reviving a proposed peace conference, the prospects for a diplomatic breakthrough appeared dim. Mr. Assad’s position is stronger, and the rebellion has grown weaker, more fragmented and more dominated by Islamic radical factions.

A close examination of how the Obama administration finds itself at this point — based on interviews with dozens of current and former members of the administration, foreign diplomats and Congressional officials — starts with a deeply ambivalent president who has presided over a far more contentious debate among his advisers than previously known. Those advisers reflected Mr. Obama’s own conflicting impulses on how to respond to the forces unleashed by the Arab Spring: whether to side with those battling authoritarian governments or to avoid the risk of becoming enmeshed in another messy war in the Middle East.

And, as the debate dragged on, the toll of civilian deaths steadily rose, Syria’s government was emboldened to use chemical weapons on a larger scale, and America’s relations with some of its closest allies were strained.

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Some of Mr. Obama’s defenders argue that, while the past two years of American policy on Syria have been messy, the events of the past six weeks have been a successful case of coercive diplomacy. Only under the threat of force, they said, has Mr. Assad pledged to give up his chemical weapons program. They argue that this might be the best outcome from a stew of bad alternatives.

“We need to be realistic about our ability to dictate events in Syria,” said Benjamin J. Rhodes, a deputy national security adviser. “In the absence of any good options, people have lifted up military support for the opposition as a silver bullet, but it has to be seen as a tactic — not a strategy.”

But others are far more critical, saying that the administration’s paralysis left it unprepared for foreseeable events like the Aug. 21 gas attack. Decisive action by Washington, they argue, could have bolstered moderate forces battling Mr. Assad’s troops for more than two years, and helped stem the rising toll of civilian dead, blunt the influence of radical Islamist groups among the rebels and perhaps even deter the Syria government from using chemical weapons.

As one former senior White House official put it, “We spent so much damn time navel gazing, and that’s the tragedy of it.”

A War Drags On

At first, the future of Syria did not seem so complicated — nobody believed that Mr. Assad would survive.

In the summer of 2011, the momentum of the Arab uprisings appeared to be sweeping all before it. Gone were the dictators of Tunisia and Egypt, and in Libya, Col. Muammar el-Qaddafi would fall later in the year.

American intelligence agencies gave regular briefings at the White House and the State Department concluding that Mr. Assad’s days were numbered, and on Aug. 18, 2011, Mr. Obama released a statement declaring that “the time has come for President Assad to step aside.”

Some in the administration worried about making such a declaration in the absence of a strategy to help make it happen. But those voices were rare.

At the time, the popular uprising was five months old, and the Syrian government’s widespread torture and killing of protesters had drawn global condemnation; some in the United States Congress had already criticized the administration for not acting yet.

But from the beginning, Mr. Obama made it clear to his aides that he did not envision an American military intervention, even as public calls mounted that year for a no-fly zone to protect Syrian civilians from bombings.

Gen. Martin E. Dempsey, the chairman of the Joint Chiefs of Staff, gave a slide-show presentation in the Situation Room in early 2012 that helped take any military option off the table. Imposing a no-fly zone, he said, would require as many as 70,000 American servicemen to dismantle Syria’s sophisticated antiaircraft system and then impose a 24-hour watch over the country.

By late summer 2012, however, American intelligence agencies began picking up communications with ominous signals that Mr. Assad’s military was moving chemical weapons and possibly mixing them in preparation for use.

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Mr. Obama ordered a series of urgent meetings, and on Aug. 20 he made a comment that would come to haunt him. Though he was determined to keep the American military out of Syria, “a red line for us is we start seeing a whole bunch of chemical weapons moving around or being utilized,” he said at a news conference. “That would change my calculus. That would change my equation.”

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In the first high-level discussion about wading into the conflict a few days later, the C.I.A. director, David H. Petraeus, presented a plan to begin arming and training small groups of rebel forces at secret bases in Jordan. Secretary of State Hillary Rodham Clinton backed Mr. Petraeus’s plan. She said it was time for the United States to get “skin in the game.” Mr. Obama went around the table asking what his aides thought about the C.I.A. plan.

Defense Secretary Leon E. Panetta and General Dempsey backed it. But others thought the proposal by Mr. Petraeus, a former four-star general who championed covert paramilitary operations, offered high risks with few rewards. Susan E. Rice, the American ambassador to the United Nations, spoke up by videophone, warning that arming the rebels would draw the United States into a murky conflict that could consume the agenda of the president’s second term and would probably make little difference on the chaotic battlefield.

Mr. Obama, who had said at the beginning of the meeting that he would make no immediate decisions, appeared skeptical. He cautioned against a “haphazard” plan to arm the rebels, and asked about tactics — who would get the weapons, how to keep them out of the hands of jihadists.

The president’s view, according to one administration official who, like others, spoke on the condition of anonymity because he was discussing debates about classified operations, seemed to be that “we’d be taking a lot of risk without a clear plan.”

Fears of a Quagmire

For Mr. Obama, the Libya precedent loomed heavily over the Syria debate. That intervention in 2011 was strictly limited in scale and scope, and had the legal imprimatur of the United Nations Security Council as well as regional and international support. Even so, the Libya campaign had dragged on for seven months and expanded from protecting civilians to engineering the ouster of Colonel Qaddafi. Mr. Obama raised Libya repeatedly in debates as an example of how difficult it would be to prevent “mission creep,” if the United States were to cross the line to military operations.

As the president and his advisers debated their options in Syria, two American allies, Qatar and Saudi Arabia, were steadily funneling money and weapons to the rebels — and urging the Obama administration to join them.

But at the State Department, some officials were fuming about what they felt was a broken process and a lack of strategy.

The administration took more than a year to nominate a replacement for Jeffrey D. Feltman, a veteran Arabic-speaking diplomat who had coordinated the State Department’s Middle East policy and left in June 2012 for a job at the United Nations. Much of the department’s time was now being devoted to what was called the “post-Assad project,” the planning for political transition in Syria. Many State Department officials began to dismiss the project as a useless academic exercise. They believed that its premise — that Mr. Assad’s government was on the verge of collapse — was becoming outdated.

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After Mr. Obama’s sweeping re-election victory, some of those officials, and others in the administration, expected a change in the White House’s position on Syria — and an end to what they saw as the stalemate of the previous year. Those expectations, however, were dashed during a meeting in early December. Michael J. Morell, who had taken over at the C.I.A. when Mr. Petraeus resigned after acknowledging an extramarital affair, renewed his predecessor’s pitch to begin arming the rebels. The agency had tinkered with the proposal made by Mr. Petraeus, partly to address directly the president’s skepticism about the plan.

Mr. Obama expressed thanks for everyone’s comments and said he wanted to think about it. One former White House official at the meeting said it was clear from Mr. Obama’s body language that he was not convinced. “They could have tweaked this thing till kingdom come, it wouldn’t have made any difference,” the official said. “He just didn’t think it was a good idea, period.”

The second term also brought a new national security team, including a secretary of state, Mr. Kerry, who came to his job convinced that the United States could step up military support to the Syrian rebels while also working with Russia to broker a diplomatic solution to the crisis.

Denis R. McDonough, the deputy national security adviser and one of the biggest skeptics about American intervention in Syria, was promoted to White House chief of staff. Mr. McDonough had clashed frequently with his colleagues on Syria policy, including with Samantha Power, a White House official who had long championed the idea that nations have a moral obligation to intervene to prevent genocide.

Ms. Power came to believe that America’s offers of support to the rebels were empty.

“Denis, if you had met the rebels as frequently as I have, you would be as passionate as I am,” Ms. Power told Mr. McDonough at one meeting, according to two people who attended.

“Samantha, we’ll just have to agree to disagree,” Mr. McDonough responded crisply.

Battlefield’s Balance Tips

But a new American intelligence assessment at the beginning of 2013 revived the discussions about whether to give arms to the rebels.

In a reversal from what spy agencies had been telling administration officials for more than a year, the new assessment concluded that Mr. Assad’s government was in no danger of collapsing, and that Syrian troops were gaining the upper hand in the civil war. The pace of Syrian Army defections had slowed, and Iranian munitions shipments had replenished the stocks of army units that had once complained of shortages in arms and ammunition.

The opposite was true for the rebels, who were running out of ammunition and supplies. Morale was low, American spy agencies concluded, and Qaeda-linked groups like the Nusra Front were becoming increasingly dominant in the rebellion.

Besides the Syrian government’s gains, there was mounting evidence that Mr. Assad’s troops had repeatedly used chemical weapons against civilians.

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Even as the debate about arming the rebels took on a new urgency, Mr. Obama rarely voiced strong opinions during senior staff meetings. But current and former officials said his body language was telling: he often appeared impatient or disengaged while listening to the debate, sometimes scrolling through messages on his BlackBerry or slouching and chewing gum.

In private conversations with aides, Mr. Obama described Syria as one of those hellish problems every president faces, where the risks are endless and all the options are bad. Those views would then be reflected in larger groups by Tom Donilon, the national security adviser, and Mr. McDonough.

“You could read the president’s position through Tom and Denis,” one former senior White House official said.

Slowly, however, Mr. Obama’s position began to change, in no small part because of intense lobbying by foreign officials. During a three-day trip to the Middle East in March, Mr. Obama met with Prime Minister Benjamin Netanyahu of Israel, who warned him that the Assad government’s chemical weapons could fall into the hands of the Lebanese militant group Hezbollah.

The pressure was even more intense the next day in Jordan, where Mr. Obama, Mr. Donilon and Mr. Kerry had a late-night dinner with King Abdullah II. Jordan was straining under the weight of more than 100,000 Syrian refugees, and the king urged Mr. Obama to take a more active role in trying to end the war.

Jordanian officials were even offering to allow the C.I.A. to use the country as a base for drone strikes in Syria — offers that the Obama administration repeatedly declined.

By April, senior officials said, one of the major skeptics, Mr. Donilon, had shifted in favor of arming the rebels. Another strong opponent in the fall, Ms. Rice, had also shifted her position, partly because of the alarming intelligence about the state of the rebellion.

Mr. McDonough, who had perhaps the closest ties to Mr. Obama, remained skeptical. He questioned how much it was in America’s interest to tamp down the violence in Syria. Accompanying a group of senior lawmakers on a day trip to the Guantánamo Bay naval base in early June, Mr. McDonough argued that the status quo in Syria could keep Iran pinned down for years. In later discussions, he also suggested that a fight in Syria between Hezbollah and Al Qaeda would work to America’s advantage, according to Congressional officials.

But debate had shifted from whether to arm Syrian rebels to how to do it. Discussions about putting the Pentagon in charge of the program — and publicly acknowledging the arming and training program — were eventually shelved when it was decided that too many legal hurdles stood in the way of the United States’ openly supporting the overthrow of a sovereign government.

Instead, Mr. Obama decided to make the rebel training program a “covert action” run by the C.I.A. He signed a secret finding allowing the agency to begin preparing to train and arm small groups of rebels in Jordan, a move that circumvented the legal issues and allowed the White House to officially deny it was giving the lethal aid.

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Besides the legal worries, there were other concerns driving the decision to make the program a secret.

As one former senior administration official put it, “We needed plausible deniability in case the arms got into the hands of Al Nusra.”

Dragging Its Feet

The president signed the finding in April, but months went by without any movement on the C.I.A. program. The White House waited to ask Congress for money for the secret mission, further evidence of Mr. Obama’s continued misgivings.

Through the spring, Iran continued to step up support for Syrian government troops, and Hezbollah fighters joined the offensive against rebel forces. The rebellion was collapsing, and a classified State Department briefing paper on June 10, which mentioned the rebel commander Gen. Salim Idris, painted a grim picture.

“We are headed toward our worst case scenario: rebel gains evaporating, the moderate opposition — including Salim Idriss — imploding, large ungoverned spaces, Asad holding on indefinitely, neighbors endangered, and Iran, Hizbollah, and Iraqi militias taking root,” the paper concluded.

With the policy on Syria foundering, Mr. Obama’s top advisers met in the Situation Room on June 12.

Mr. Kerry had recently announced a deal with his Russian counterpart, Sergey V. Lavrov, to hold an international peace conference in Geneva to try to end the fighting. But rebel setbacks had cooled any enthusiasm for talks among many American officials at a time when Mr. Assad held all the leverage and leading opposition figures were refusing to attend.

“We need to go slow on Geneva given the SOC’s disarray and the worsening situation on the ground,” said a sheet of talking points, referring to the Syrian opposition coalition, prepared for Mr. Kerry to take to the meeting.

And the administration faced another problem. There was no longer doubt among American intelligence agencies that Syrian troops had repeatedly used chemical weapons against civilians. With the president’s “red line” having been crossed, the White House had to come up with a public pronouncement that showed it was prepared to enforce consequences. What came next was a surprise across the government, from the Pentagon to the State Department to the C.I.A.

The day after the meeting, Mr. Rhodes held a news conference and told reporters that Mr. Obama had made a decision — a decision that actually had been made two months earlier and that would be carried out in secret as a C.I.A. covert action. Mr. Rhodes said the United States would give additional military support to the rebels, although he refrained from spelling out that it would involve arming and training them, and that the C.I.A. would supervise the effort.

Mr. Obama made no public statement on the issue.

A Surprising About-Turn

An administration that had spent nearly two years telling members of Congress it was determined to avoid direct military intervention in Syria now had to persuade lawmakers to pay for the arming and training program.

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The lobbying began, with Mr. Kerry holding closed meetings with the House and Senate Intelligence Committees. Immediately, he was deluged with questions from both Republicans and Democrats: How would he ensure that arms did not fall into the hands of Islamic extremists? Would arming the rebels tip the balance on the battlefield? What was the overall strategy?

It took weeks to overcome skepticism on Capitol Hill, but the intelligence committees eventually approved the administration’s plan to give light arms to the rebels, but not the antiaircraft weapons the rebels insisted they needed the most. But the Aug. 21 poison gas attack on the outskirts of Damascus changed those plans — and suddenly put Syria, for the first time, on top of the president’s agenda.

Within hours, administration officials began signaling that they were preparing for an immediate military strike to punish the Syrian government — an idea dismissed repeatedly in the past and a hard sell with some allies, a war-weary public and Congress. But after the British declined to participate in the operation, and Mr. Obama abruptly decided he would seek Congressional support for the strike, many lawmakers were led to suspect that Mr. Obama still was not convinced that intervention was a good idea.

A senior White House official said that one reason the president had decided to get Congressional approval was his fear that alienating lawmakers might undermine their support on other tough foreign policy issues, most notably Iran. In early July, Mr. Obama had asked Ms. Rice, who had succeeded Mr. Donilon as national security adviser, to undertake a review of American policy in the Middle East and North Africa, and to make Syria part of a broader strategy involving both Iran and the Middle East peace process.

Two days after his announcement that he would go to Congress for approval of a strike, Mr. Obama met in the Oval Office with Senators John McCain of Arizona and Lindsey Graham of South Carolina, the two Republicans who are the Senate’s most outspoken advocates of military intervention in Syria. Mr. Obama agreed with the senators that American efforts to arm the rebels had been slow, but told them that the first group of 50 Syrian rebels — trained by the C.I.A. in Jordan — would soon cross into Syria, according to sources familiar with the meeting.

The goal was for that group to train larger numbers of rebels in Syria — expanding the impact of the limited C.I.A. training effort in Jordan. But Mr. Obama acknowledged that having the C.I.A. carry out the training covertly had slowed the pace of the program and suggested that he was considering expanding the program and carrying it out publicly, an allusion to having the Pentagon take over.

The president’s enthusiasm for that approach soon cooled again. A week after the meeting with the two senators, Mr. Obama seized on a proposal by President Vladimir V. Putin of Russia, aimed at forcing the Syrian government to give up its chemical weapons stockpiles. That effort, adopted by the Security Council in late September, appears to have overshadowed the arming project.

While the training mission in Jordan continues, officials now say there is no immediate plan to drastically expand it under the Pentagon’s control. The White House appears to be concerned that a public effort might undermine the diplomatic initiative to remove Syria’s chemical weapons stockpiles and convene a peace conference. Mr. Assad, meanwhile, told a Lebanese newspaper in mid-October that he was happy to trade his chemical arsenal, which he dismissed as “obsolete,” in order to “spare Syria” from aggression by the United States.

During his Senate confirmation hearing this month, the Obama administration’s nominee to run special operations policy at the Pentagon was asked whether the rebel training program — currently run by the C.I.A. — might significantly change the balance of power in Syria.

The nominee, Michael D. Lumpkin, a former member of the Navy SEALs, was candid in his answer.

It would not, he said.