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BENGHAZI, Libya — A boyish-looking U.S. diplomat was meeting for the first time with the Islamist leaders of eastern Libya’s most formidable militias.

It was Sept. 9, 2012. Gathered on folding chairs in a banquet hall by the Mediterranean, the Libyans warned of rising threats against Americans from extremists in Benghazi. One militia leader, with a long beard and mismatched military fatigues, mentioned time in exile in Afghanistan. A U.S. guard discreetly touched his gun.

“Since Benghazi isn’t safe, it is better for you to leave now,” Mohamed al-Gharabi, leader of the Rafallah al-Sehati Brigade, recalled telling the Americans. “I specifically told the Americans myself that we hoped they would leave Benghazi as soon as possible.”

Yet as the militiamen snacked on Twinkie-style cakes with their U.S. guests, they also gushed about their gratitude for President Obama’s support in their uprising against Moammar Gadhafi. They emphasized they wanted to build a partnership with the United States, especially in the form of more investment. They specifically asked for Benghazi outlets of McDonald’s and KFC.

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The diplomat, David McFarland, a former congressional aide who had never before met with a Libyan militia leader, left feeling agitated, according to colleagues. But the meeting did not shake his faith in the prospects for deeper involvement in Libya.

Two days later, he summarized the meeting in a cable to Washington, describing a mixed message from the militia leaders.

Despite “growing problems with security,” he wrote, the fighters wanted the United States to become more engaged “by ‘pressuring’ American businesses to invest in Benghazi.”

The cable, dated Sept. 11, 2012, was sent over the name of McFarland’s boss, Ambassador J. Christopher Stevens.

Later that day, Stevens was dead, killed with three other Americans — U.S. Mission information officer Sean Smith and security guards Tyrone Woods and Glen Doherty — in Benghazi in the most significant attack on U.S. property in 11 years, since Sept. 11, 2001.

The cable was a last token of months of American misunderstandings and misperceptions about Libya and especially Benghazi, many fostered by shadows of the earlier Sept. 11 attack.

The video factor

The United States waded deeply into post-Gadhafi Libya, hoping to build a beachhead against extremists, especially al-Qaida. It believed it could draw a bright line between friends and enemies in Libya.

But it ultimately lost its ambassador in an attack that involved both avowed opponents of the West and fighters belonging to militias that the Americans had taken for allies.

Months of investigation by The New York Times, centered on extensive interviews with Libyans in Benghazi who had direct knowledge of the attack there and its context, turned up no evidence that al-Qaida or other international terrorist groups had any role in the assault.

The attack was led, instead, by fighters who had benefited directly from NATO’s extensive air power and logistics support during the uprising against Gadhafi.

And contrary to claims by some members of Congress, it was fueled in large part by anger at a video made in the U.S. that denigrated Islam.

A fuller accounting of the attacks suggests lessons for the United States that go well beyond Libya. It shows the risks of expecting U.S. aid in a time of desperation to buy durable loyalty, and the difficulty of discerning friends from allies of convenience in a culture shaped by decades of anti-Western sentiment.

The attack also suggests that, as the threats from local militants in the region have multiplied, an intensive focus on combating al-Qaida may distract from safeguarding U.S. interests.

In this case, a central figure in the attack was an eccentric, malcontent militia leader, Ahmed Abu Khattala, according to numerous Libyans present at the time. U.S. officials briefed on the criminal investigation into the killings call him a prime suspect.

Abu Khattala declared openly and often that he placed the United States not far behind Gadhafi on his list of infidel enemies. But he had no known affiliations with terrorist groups, and he had escaped scrutiny from the 20-person CIA station in Benghazi set up to monitor the local situation.

Abu Khattala, 42, who denies participating in the attack, was firmly embedded in the network of Benghazi militias before and afterward. Many other Islamist leaders consider him an erratic extremist.

But he was never more than a step removed from the most influential commanders who dominated Benghazi and who befriended the Americans. They were his neighbors, his fellow inmates and his comrades on the front lines in the fight against Gadhafi.

Fifteen months after Stevens’ death, the question of responsibility remains a searing issue in Washington, framed by two contradictory story lines.

One has it that the video, which was posted on YouTube, inspired spontaneous street protests that got out of hand. This version, based on early intelligence reports, was initially offered publicly by Susan Rice, who is now Obama’s national-security adviser.

The other, favored by Republicans, holds that Stevens died in a carefully planned assault by al-Qaida to mark the anniversary of its strike on the United States 11 years before. Republicans have accused the Obama administration of covering up evidence of al-Qaida’s role to avoid undermining the president’s claim that the group has been decimated.

The investigation shows that the reality in Benghazi was different, and murkier, than either of those story lines suggests. Benghazi was not infiltrated by al-Qaida, but nonetheless contained grave local threats to U.S. interests. The attack does not appear to have been meticulously planned, but neither was it spontaneous or without warning signs.

Focus on al-Qaida

Abu Khattala had become well-known in Benghazi for his role in the killing of a rebel general, and then for declaring that his fellow Islamists were insufficiently committed to theocracy. He made no secret of his readiness to use violence against Western interests.

One of his allies, the leader of Benghazi’s most overtly anti-Western militia, Ansar al-Shariah, boasted a few months before the attack that his fighters could “flatten” the U.S. Mission. Surveillance of the U.S. compound appears to have been under way at least 12 hours before the assault started.

The violence, though, also had spontaneous elements. Anger at the video motivated the initial attack. Dozens of others joined in, some of them provoked by the video and others responding to fast-spreading false rumors that guards inside the U.S. compound had shot Libyan protesters.

Looters and arsonists, without any sign of a plan, were the ones who ravaged the compound after the initial attack, according to more than a dozen Libyan witnesses and many U.S. officials who have viewed the footage from security cameras.

The Benghazi-based CIA team had briefed McFarland and Stevens as recently as the day before the attack. But the U.S. intelligence efforts in Libya focused on the agendas of the biggest militia leaders and the handful of Libyans with suspected ties to al-Qaida, several officials who got the briefings said.

Like virtually all briefings over that period, the one that day made no mention of Abu Khattala, Ansar al-Shariah or the video ridiculing Islam, even though Egyptian satellite-television networks popular in Benghazi were spewing outrage against it.

Members of the local militia groups the Americans called on for help proved unreliable, even hostile. The fixation on al-Qaida may have distracted experts from more imminent threats. Those now look like intelligence failures.

More broadly, Stevens, like his bosses in Washington, believed the United States could turn a critical mass of the fighters it helped oust Gadhafi into reliable friends. He died trying.

A fuse is lit

The video Rice referred to, “Innocence of Muslims,” purported to be an online trailer for a film about the mistreatment of Christians in contemporary Egypt. But it included bawdy historical flashbacks that derided the Prophet Muhammad.

Someone dubbed it into Arabic around the beginning of September 2012, and a Cairo newspaper embellished the news by reporting that a Florida pastor infamous for burning the Quran was planning to debut the film on the 11th anniversary of the 2001 terrorist attacks.

Then, on Sept. 8, a popular Islamist preacher lit the fuse by screening a clip of the video on the ultraconservative Egyptian satellite channel El Nas. U.S. diplomats in Cairo raised the alarm in Washington about a growing backlash, including calls for a protest outside their embassy.

No one mentioned it to the U.S. diplomats in Libya. But Islamists in Benghazi were watching. Egyptian satellite networks like El Nas and El Rahma were widely available in Benghazi.

By Sept. 9, a popular eastern Libyan Facebook page had denounced the film. On the morning of Sept. 11, even some secular political activists were posting calls online for a protest that Friday, three days away.

Hussein Abu Hamida, acting chief of Benghazi’s informal police force, saw the growing furor and feared new violence against Western interests.

He conferred with Abdul Salam Bargathi of the Preventive Security Brigade, an Islamist militia with a grandiose name, each recalled separately, and they increased security outside a U.N. office. But they said nothing to the Americans.

Reports of the video, made by an Egyptian-born Coptic Christian living in Los Angeles, were just beginning to spread Sept. 9 when McFarland, the officer normally in charge of politics and economics at the U.S. Embassy in Tripoli, met with the Benghazi militia leaders.

Among them were some of the same men who had greeted Stevens when he arrived in Benghazi at the start of the revolt, including al-Gharabi, 39, who ran a local sandwich truck before becoming the leader of the Rafallah al-Sehati.

Another was Wissam bin Hamid, also 39, a slim and slightly hunched mechanic known for his skill with American cars who by then had become the leader of Libya Shield, seen as one of Libya’s strongest militias.

In an interview, al-Gharabi said he had known about the rage in Egypt over the video, but: “We did not know if it was going to reach us here.”

McFarland seemed most concerned about the big militia leaders. “ ‘How do the revolutionaries feel about having relationships with Western countries? What is your opinion about the United States?’ ” the Americans asked, according to al-Gharabi. It was “an interrogation,” he said.

“We told them that we hoped that the countries which helped us during the war would now help us in development,” he said. “And America was at the top of the pyramid.”

Al-Gharabi and two other Libyan militia leaders present said separately that they tried to warn McFarland. “We told them: ‘Weapons are everywhere, in every home, and there is no real control,’ ” bin Hamid said.

McFarland struggled to make sense of their contradictory signals. “The message was, ‘Don’t come here because there is no security, but come right away because we need you,’” McFarland later told colleagues.

The militia leaders seemed unable to get their stories straight, his colleagues said, and the vague warnings amounted to a reminder of what the diplomats already knew: Post-revolutionary Benghazi was a dangerous place.

Back in Washington

After the attack, Obama vowed retribution. “We will not waver in our commitment to see that justice is done for this terrible act,” he said in a televised address from Washington on Sept. 12. “And make no mistake, justice will be done.”

But much of the debate about Benghazi in Washington has focused on statements made four days later in television interviews by Rice, then ambassador to the United Nations.

“What happened in Benghazi was in fact initially a spontaneous reaction to what had just transpired hours before in Cairo,” she said on NBC’s “Meet the Press,” “almost a copycat of the demonstrations against our facility in Cairo, prompted by the video.”

Republicans, pouncing on the misstatement, have argued the Obama administration was trying to cover up al-Qaida’s role. “It was very clear to the individuals on the ground that this was an al-Qaida-led event,” Rep. Mike Rogers, R-Mich., chairman of the House Intelligence Committee, said last month on Fox News.

But the Republican arguments appear to conflate purely local extremist groups like Ansar al-Shariah with al-Qaida’s international terrorist network.

The only intelligence connecting al-Qaida to the attack was an intercepted phone call that night from a participant in the first wave of the attack to a friend in another African country who had ties to members of al-Qaida, said several officials briefed on the call. But when the friend heard the attacker’s boasts, he sounded astonished, the officials said, suggesting he had no prior knowledge of the assault.

Al-Qaida was having its own problems penetrating the Libyan chaos. Three weeks after the attack, on Oct. 3, 2012, leaders of the group’s regional affiliate, al-Qaida in the Islamic Maghreb, sent a letter to a lieutenant about efforts to crack the new territory.

The leaders said they had sent four teams to try to establish footholds in Libya. But of the four, only two in the southern Sahara “were able to enter Libyan territory and lay the first practical bricks there,” the letter said.

The letter, left behind when the group’s leaders fled French troops in Mali, was later obtained and released by The Associated Press.

In the days after the Benghazi attack, meanwhile, Abu Khattala was moving at ease around the city, even mocking the U.S. political debate about the ambassador’s death.

“It is always the same two teams, but all that changes is the ball,” he said in an interview. “They are just laughing at their own people.”

He suggested the video insulting the Prophet Muhammad might well have justified the killing of four Americans. “From a religious point of view, it is hard to say whether it is good or bad,” he said.

By summer, U.S. investigators had interviewed hundreds of witnesses and formally asked the Libyan government to arrest Abu Khattala, along with about a dozen others wanted for questioning. The U.S. military also prepared a plan to capture him on its own, officials said.

But the administration held back, fearing that unilateral U.S. military action could set off a backlash that would undermine the fragile Libyan government.

Hearing rumors that a revenge-seeking mob was threatening to come after Abu Khattala this fall, dozens of his neighbors sprang to his defense. Fighters raced to erect checkpoints around his house, and they pulled out Kalashnikovs, grenade launchers, truck-mounted artillery and even a tank.

Al-Gharabi said Libya’s prime minister, under pressure from the Americans, had asked a Benghazi army commander for help apprehending Abu Khattala.

Al-Gharabi quoted the commander as replying, “You will be lucky if he does not apprehend you.”

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