By SCOTT SHANE and JO BECKER

New York Times

It was a grisly start to the new era for Libya, broadcast around the world. The dictator was dragged from the sewer pipe where he was hiding, tossed around by frenzied rebel soldiers, beaten bloody and sodomized with a bayonet. A shaky cellphone video showed the pocked face of Moammar Gadhafi, “the Leader” who had terrified Libyans for four decades, looking frightened and bewildered. He would soon be dead.

The first news reports of Gadhafi’s capture and killing in October 2011 reached the secretary of state in Kabul, Afghanistan, where she had just sat down for a televised interview. “Wow!” she said, looking at an aide’s BlackBerry before cautiously noting that the report had not yet been confirmed. But Hillary Clinton seemed impatient for a conclusion to the multinational military intervention she had done so much to organize, and in a rare unguarded moment, she dropped her reserve.

“We came, we saw, he died!” she exclaimed.

Two days before, Clinton had taken a triumphal tour of the Libyan capital, Tripoli, and for weeks top aides had been circulating a “ticktock” that described her starring role in the events that had led to this moment. The timeline, her top policy aide, Jake Sullivan, wrote, demonstrated Clinton’s “leadership/ownership/stewardship of this country’s Libya policy from start to finish.” The memo’s language put her at the center of everything: “HRC announces … HRC directs … HRC travels … HRC engages,” it read.

It was a brag sheet for a Cabinet member eyeing a presidential race, and the Clinton team’s eagerness to claim credit for her prompted eye-rolling at the White House and the Pentagon. Some joked that to hear her aides tell it, she had practically called in the airstrikes herself.

But there were plenty of signs that the triumph would be short-lived, that the vacuum left by Gadhafi’s death invited violence and division.

In fact, on the same August day that Sullivan had compiled his laudatory memo, the State Department’s top Middle East hand, Jeffrey D. Feltman, had sent a lengthy email with an utterly different tone about what he had seen on his own visit to Libya.

The country’s interim leaders seemed shockingly disengaged, he wrote. Mahmoud Jibril, the acting prime minister, who had helped persuade Clinton to back the opposition, was commuting from Qatar, making only “cameo” appearances. A leading rebel general had been assassinated, underscoring the hazard of “revenge killings.” Islamists were moving aggressively to seize power, and members of the anti-Gadhafi coalition, notably Qatar, were financing them.

On a task of the utmost urgency, disarming the militia fighters who had dethroned the dictator but now threatened the nation’s unity, Feltman reported an alarming lassitude. Jibril and his associates, he wrote, “tried to avert their eyes” from the problem militias could pose on “the Day After.”

In short, the well-intentioned men who now nominally ran Libya were relying on “luck, tribal discipline and the ‘gentle character’ of the Libyan people” for a peaceful future. “We will continue to push on this,” he wrote.

In the ensuing months, Feltman’s memo would prove hauntingly prescient. But Libya’s Western allies, preoccupied by domestic politics and the crisis in Syria, would soon relegate the country to the back burner.

And Clinton would be mostly a bystander as the country dissolved into chaos, leading to a civil war that would destabilize the region, fueling the refugee crisis in Europe and allowing the Islamic State to establish a Libyan haven that the United States is now desperately trying to contain.

“Nobody will say it’s too late. No one wants to say it,” said Mahmud Shammam, who served as chief spokesman for the interim government. “But I’m afraid there is very little time left for Libya.”

‘What Else Can You Do?’

Media reports referred to Clinton’s one brief visit to Libya in October 2011 as a “victory lap,” but the declaration was decidedly premature. Security precautions were extraordinary, with ships positioned off the coast in case an emergency evacuation was needed. As it turned out, there was no violence. But the wild celebratory scenes in the Libyan capital that day actually highlighted the divisions in the new order.

At a hospital, a university and government offices, Clinton posed for photos with the Western-educated interim leaders and hailed the promise of democracy.

“I am proud to stand here on the soil of a free Libya,” she declared, standing alongside a beaming Jibril. “It is a great privilege to see a new future for Libya being born. And indeed, the work ahead is quite challenging, but the Libyan people have demonstrated the resolve and resilience necessary to achieve their goals.”

But everywhere Clinton went, there was the other face of the rebellion. Crowds of Kalashnikov-toting fighters — the thuwar, or revolutionaries, as they called themselves — mobbed her motorcade and pushed to glimpse the U.S. celebrity. Mostly they cheered, and Clinton remained poised and unrattled, but her security detail watched the pandemonium with white-knuckled concern.

At the University of Tripoli, students were trampling wall hangings of Gadhafi that had been pulled to the ground, recalled Harold Koh, the State Department’s top lawyer, who had flown in with Clinton on a U.S. military aircraft. One grateful student pointed out the gallows where anti-Gadhafi protesters had been hanged, while others wondered what the United States might do to help win the peace.

“We know what the U.S. can do with bombs,” one student told Koh. “What else can you do?”

When Clinton’s entourage finally departed, Gene A. Cretz, the U.S. ambassador, wrote a relieved email to Cheryl Mills, the secretary of state’s chief of staff. The visit, he wrote, had been “picture perfect given the chaos we labor under in Libya.”

Clinton certainly understood how hard the transition to a post-Gadhafi Libya would be. In February, before the allied bombing began, she noted that political change in Egypt had proved tumultuous despite strong institutions.

“So imagine how difficult it will be in a country like Libya,” she had said. “Gadhafi ruled for 42 years by basically destroying all institutions and never even creating an army, so that it could not be used against him.”

Early on, the president’s national security adviser, Tom Donilon, had created a planning group called “Post-Q.” Clinton helped organize the Libya Contact Group, a powerhouse collection of countries that had pledged to work for a stable and prosperous future. By early 2012, she had flown to a dozen international meetings on Libya, part of a grueling schedule of official travel in which she kept competitive track of miles traveled and countries visited.

Dennis B. Ross, a veteran Middle East expert at the National Security Council, had argued unsuccessfully for an outside peacekeeping force. But with oil beginning to flow again from Libyan wells, he was pleasantly surprised by how things seemed to be going.

“I had unease that there wasn’t more being done more quickly to create cohesive security forces,” Ross said. “But the last six months of 2011, there was a fair amount of optimism.”

Even so, the gulf separating the suave English speakers of the interim government from the thuwar was becoming more and more pronounced.

After decades in exile, some leaders were more familiar with U.S. and European universities than with Libyan tribes and the militias that had sprung from them. Others, like Jibril, were suspect in some quarters because of previous roles in the Gadhafi regime. It was increasingly evident that the ragtag populist army that had actually done the fighting against Gadhafi was not taking orders from the men in suits who believed they were Libya’s new leaders.

“It should have been clear to anyone,” said Mohammed Ali Abdallah, an opposition member who now heads a leading political party, “that there were clear contradictions in the makeup of the opposition and that unity could not last.”

Jeremy Shapiro, who handled Libya on Clinton’s policy staff, said the administration was looking for “the unifier — the Nelson Mandela.” He added: “That was why Jibril was so attractive. We were always saying, ‘This is the guy who can appeal to all the factions.’ What we should have been looking for — but we were never good at playing that game — is a power balance.”

Under the circumstances, Libya’s push for elections by July 2012, nine months after Gadhafi’s death, appeared to some to be premature. But the schedule fulfilled the opposition’s promises to the West and had the backing of competing factions.

“Suddenly you had people who belonged to political parties,” said Abdurrazag Mukhtar, a member of the interim government who lived in California for many years and is now Libya’s ambassador to Turkey. “The Muslim Brotherhood. Jibril. All these guys thinking, ‘Time for an election.’”

“But we were not ready,” he said. “You needed a road map for security first.”

‘Fierce Limits’

By January 2012, there was an unmistakable drumbeat of trouble.

His popularity sagging, Jibril had stepped down as transitional prime minister. A prominent Muslim scholar had accused him of guiding the nation toward a “new era of tyranny and dictatorship.” In a deal struck between two powerful militias, he was replaced by Abdurrahim el-Keib, an engineering professor who had taught for years at the University of Alabama.

On Jan. 5, Clinton’s old friend and adviser Sidney Blumenthal emailed her with the latest in a series of behind-the-scenes reports on Libya, largely written by a retired CIA officer, Tyler Drumheller, who died last year.

The memo detailed the roiling tensions between Islamists and secularists over the role of Islamic law, fighting between rival militias associated with two different towns and four visits to el-Keib’s office by “angry militiamen” demanding concessions.

El-Keib, the email said, “believes that if he does not disarm the militias and meet their demands in the next six months, there is a good chance of increased fighting among rival groups that could lead to civil war.” Clinton forwarded the message to Sullivan, her policy aide, with a single comment: “Worrying.”

Such alarming reports might have been expected to spur action in Washington. They did not.

After Gadhafi’s fall, with minimal violence and friendly interim leadership, Libya had moved quickly off the top of the administration’s agenda. The regular situation room meetings on Libya, often including the president, simply stopped. The revolt in Syria, in the heart of the Middle East and with nearly four times Libya’s population, took center stage.

Libya, Ross said, “was farmed out to the working level.”

The inattention was not just neglect. It was policy.

“The president was like, ‘We are not looking to do another Iraq,’” said Derek Chollet, then handling Libya for the National Security Council. “And by the way, the Europeans were all along saying: ‘No, no, no, we’re doing this. We got it. We believe in Libya. This is in our neighborhood.’”

So the president and the National Security Council set what one official called “fierce limits” on the U.S. role: The United States would provide help only when it could offer a unique capability, only when Libya explicitly requested the services and only when Libya paid for them with its oil revenue. In practice, those conditions meant the United States would do very little.

And though the French president, Nicolas Sarkozy, and the British prime minister, David Cameron, visited Libya together, they, too, were soon distracted, by re-election campaigns and economic worries.

The neglect was made easier by the Libyans themselves. Displaying both naiveté and nationalism, the interim leaders insisted, at least in public, that they wanted no outside interference. They were so wary of foreign troops that they refused to let the United Nations maintain a basic security force to protect its compound.

“They were very keen to take responsibility for their country,” Shapiro said. “And we were very keen to let them, for our own reasons. So there was a sort of conspiracy there.”

As the months passed and the factional fighting grew worse, Clinton pressed for the administration to do more, asking the Pentagon, for example, to help train security forces. But she was boxed in by the president’s strictures and the Libyans’ resistance.

“It’s like you’re twisting yourself into a pretzel to try to say, ‘OK, we won’t have boots on the ground, but we know we got to do something,’” Ross said.

Even modest proposals foundered. When Clinton proposed sending a hospital ship to treat wounded Libyan fighters, the National Security Council rejected the idea, aides said.

But whatever her misgivings, Clinton prized her relationship with the president and respected his authority to set policy. So she went along, as disciplined as ever.

‘Lost From the Beginning’

Andrew Shapiro was trying to make the best of a bad situation. He had to explain what the United States was doing to secure the vast military arsenal Gadhafi had left behind — a notable exception to the hands-off policy.

Speaking in Washington in February 2012, Shapiro, assistant secretary of state for political-military affairs, described efforts to “galvanize an international response” to find and destroy arms caches. But he acknowledged that the $40 million program Clinton had announced was not going as well as hoped, even when it came to the most worrisome weapons, the MANPADS, shoulder-fired missiles capable of shooting down an airliner.

“How many are still missing? The frank answer is we don’t know and probably never will,” Shapiro said. “We cannot rule out that some weapons may have leaked out of Libya.”

The covert coals-to-Newcastle effort to arm the rebels during the revolution was the least of it. The dictator had stashed an astonishing quantity of weapons in the desert.

“We knew he had a lot, but he had 10 times that,” said Jean-David Levitte, then a top aide to Sarkozy.

While the CIA moved quickly to secure Gadhafi’s chemical weapons, other efforts fell short. “There was one arsenal that we thought had 20,000 shoulder-fired, surface-to-air missiles, SA-7s, that basically just disappeared into the maw of the Middle East and North Africa,” recalled Robert M. Gates, the U.S. defense secretary at the time.

When it came to securing weapons, the Americans’ initial idea — to give the interim government assistance to buy them back itself — foundered when the Libyan ministers failed to carry out the program, several Libyan officials said.

So the State Department, working with the CIA, was left to try to strike its own deals with the militias. But there was little incentive to sell. As Shammam, the former spokesman for the interim government, put it: “How are you going to buy a Kalashnikov for $1,000? With a Kalashnikov, someone can make $1,000 a day kidnapping people.”

Worse, the program created an incentive for militias to import weapons to sell to the Americans, said Ali Zeidan, an adviser to the interim government who would inherit the problem in November 2012 when he became prime minister.

“If you want to buy weapons, you have to control the border,” Zeidan said, adding that the failure to do that led fighters to “sell them, get more and sell them again.”

‘Very Simple Dreams’

While the Americans struggled against weapons proliferation and hoped for the best, a former rebel officer took on the problem at the core of Libya’s predicament: disbanding the volatile forces that had ousted Gadhafi and helping the fighters find a place in a peaceful new Libya. The officer, M. Mustafa El Sagezli, would never meet Clinton. But the outcome of his lonely campaign would decide to a considerable degree Libya’s place in her record as secretary of state.

As deputy commander of the February 17 Martyrs Brigade, one of the largest and most capable rebel militias, Sagezli had tried his best to look after his recruits. It was, he felt, an obligation that did not end with the revolution.

Shortly after Gadhafi was killed, Sagezli had gathered a group of fighters in Benghazi. A businessman with degrees from Utah State University and the London School of Economics, he knew the rebel militias had been organized along Libya’s deepest fault lines: tribal divisions, regional loyalties and differing stances on Islam’s proper role. Yet the country could not progress unless the militias were reintegrated into civil society and replaced by a regular army.

“What do you need?” he asked the fighters. “What are your dreams?”

Their modest answers surprised and encouraged him.

“Some were very simple dreams,” he said. “‘Help us get married.’ Some wanted a scholarship.”

The transitional government soon set up a Warriors Affairs Commission, headed by Sagezli. Many of the 162,000 former fighters it registered were illiterate and needed education. Some wanted to join a police force or a new army, but nearly half hoped to start small businesses.

Sagezli said he had taken a proposal to the transitional government: The Labor Ministry could help would-be businessmen, the Interior Ministry could train customs and police officers, the Defense Ministry would absorb others into a national army, and so on.

It was ambitious, but the government had plenty of money; Clinton had worked hard to free up billions of dollars in Libyan assets that had been frozen by anti-Gadhafi sanctions. Her view, said one top aide, was that if the interim government “couldn’t rule by force, let them rule by finance.”

But instead of giving priority to demobilizing the militias, as an aide said Clinton had hoped, the transitional regime simply began paying fighters salaries that many viewed as protection money. In one illustrative incident in May 2012, Kikla militiamen stormed the office of el-Keib, the interim prime minister, demanding back pay as gunfire filled the air.

“Don’t give them salaries for nothing,” Sagezli recalls begging. “Giving a commander money means giving strength to the militias, more loyalty for the commander, more armaments and more corruption. They never listened.” Instead, he said, “the politicians started bribing them to buy loyalty.”

With the July elections, precedent became political imperative.

In the run-up to the vote, a powerful militia shut down roads to press its demand that its eastern Libyan region have a greater say when the incoming Parliament drafted a constitution. The authorities capitulated, leaving the writing of the constitution for a second assembly to be elected later, with more seats from the east.

That, in turn, made it harder to disarm the militias, since each faction and town knew its weapons might be needed to protect its interests in the constitutional process. That was how the game would be played.

Zeidan, who became prime minister in November 2012, financed a few of Sagezli’s programs. But he continued to pay off militia leaders. Political parties aligned themselves with various commanders, and with no army or police force to carry out their will, the elected officials became increasingly dependent on the fighters extorting them.

Haig Melkessetian, a former U.S. intelligence operative whose company provided security for European embassies in Libya, described militia rule as “anarchy — there’s just no other word for it.”

“We had to have five or six IDs to be able to pass, depending on the street,” he said.

Assassinations and “the worst kind of vigilantism” became commonplace, said Sarah Leah Whitson, who was tracking abuses in Libya for Human Rights Watch. One militia leader told her, “The GNC may have had electoral legitimacy, but we have revolutionary legitimacy.”

Sagezli said he had discussed the difficulties with U.N. representatives and with the new U.S. ambassador, J. Christopher Stevens. “I kept asking them for support,” he recalled.

But if there was any pressure from U.S. or European officials to stop the government payoffs, he said, “it wasn’t loud enough.”

‘Things Could Not Go Right’

On Aug. 8, 2012, a month after the elections, Stevens, the U.S. ambassador, signed off on a cable sent to Washington titled “The Guns of August,” playing on the title of a classic history of the first days of World War I. It described Benghazi as moving “from trepidation to euphoria and back as a series of violent incidents has dominated the political landscape” and warned of “a security vacuum.”

No U.S. official knew Libya better. He would pay with his life for his determination to see Libya’s tumultuous reality up close. A month after the cable was sent, Islamist extremists attacked the U.S. mission in Benghazi, and Stevens was one of four Americans killed.

In the assaults on the diplomatic compound and nearby CIA annex, the most worrisome trends in the country came together: the feeble central government, the breakdown of law and order, the rise of militants and the months of minimal attention from Washington. Republicans quickly seized on the episode for what would become years of inquiries, hearings and fundraising focused on Clinton.

Still, in her last months at the State Department, Clinton rode a wave of popularity, bolstered by an Internet meme called “Texts From Hillary.” Its emblem was a photograph of the secretary of state gazing through dark glasses at her BlackBerry. Few knew that it had been taken aboard the military transport plane taking her to Libya in those heady days after the dictator’s fall.

If the attempt to pin blame for the Benghazi attack on Clinton would largely fail, the notion that the Libyan intervention was among her successes had become steadily more threadbare. Libya would not conform, either as cudgel or brag, to the needs of U.S. politics.

As she exited the State Department in February 2013, factional violence, which would break into open civil war in 2014, was on the rise. The flow of refugees paying smugglers for a hazardous trip across the Mediterranean was swelling. And the Libyan chaos would give rise to two rival governments — one backed by Egypt and the United Arab Emirates, the other by Qatar, Turkey and Sudan — providing sanctuary to extremists, soon to be joined by emissaries of the Islamic State.

The weapons that had made it so hard to stabilize Libya were turning up in Syria, Tunisia, Algeria, Mali, Niger, Chad, Nigeria, Somalia, Sudan, Egypt and Gaza, often in the hands of terrorists, insurgents or criminals.

In fall 2012, U.S. intelligence agencies produced a classified assessment of the proliferation of arms from Libya. “It was like, ‘Oh, my God,’” said Michael T. Flynn, then head of the Defense Intelligence Agency. “We’ve not had that kind of proliferation of weapons since really the end of the Vietnam War.”

A cynical line would begin to circulate in Washington: In Iraq, the United States had intervened and occupied — and things had gone to hell. In Libya, the United States had intervened but not occupied — and things had gone to hell. And in Syria, the United States had neither intervened nor occupied — and things had still gone to hell.

It was a dark jest designed to shift blame from baffled U.S. policymakers to a troubled region. But it raised a serious question about Libya: If overthrowing a hated dictator in a small and relatively rich country produced such epic troubles, was U.S. intervention ever justified?

“It’s true that things went wrong,” said Sagezli, of the warriors commission. “But from a Libyan point of view, things could not go right. We had 42 years of Gadhafi’s rule, no infrastructure, a terrible education system, thousands of political prisoners, divisions among tribes, destruction of the army. When you have such a state, when you take out the dictator, it’s like taking the cover off the pot.”