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Christopher Stevens, the U.S. ambassador to Libya, smiles at his home in Tripoli June 28, 2012.ESAM OMRAN AL-FETORI/Reuters

Benghazi, Libya's second city and the capital of the oil-rich and formerly independent eastern state of Cyrenaica, has always been the place where explosions are sparked.

It was in this rough-and-tumble beachfront city that Colonel Moammar Gadhafi was first inspired to mount a military coup in the 1960s. It was here where Islamist forces were crushed brutally by Col. Gadhafi in the 1980s and '90s. It was here, on Feb. 17 last year, where the uprising against him began, and where the rebels then based their makeshift military headquarters.

So it was perhaps not surprising that it was here that eastern Libya displayed its potential for extremist violence on Tuesday night when the U.S. ambassador was killed, apparently by rocket-propelled grenades, during a protest at the consulate against an obscure Internet video.

I spent long periods in 2011 in Benghazi and its nearby military frontlines and redoubts, and after the modern and far more secular surroundings of Tripoli and the West (where most Libyans live), it felt like a dangerous place where religious forces wield a heavy hand.

It was during this period that I met John Christopher Stevens, a cool-headed American career diplomat who had just been appointed as the U.S. representative – and de facto ambassador – to the National Transitional Council, the fractious rebel government-in-waiting based in Benghazi.

In off-record briefings, he was an exceptionally calm and self-assured voice of confidence in the revolution's project, drawing on what appeared to be a deep personal understanding of Arab politics, cultures and factions to explain the deeply layered and contradictory conglomeration of movements that his government had decided to back fully.

This was far from a conventional diplomatic assignment. While the NTC surprised many observers with its organizational coherence and cooperation with the West, beneath the surface it was often a shambles, with internal factions battling one another politically and sometimes physically. Religious factions – Islamists, Salafists, and sometimes outright jihadis – often seemed to dominate the resistance, and their militias were the best funded and most organized in the east.

On the streets of Benghazi, it seemed certain that Libya's future would be Islamist. After all, the revolution had its beginnings in a Feb. 17, 2011, protest in Benghazi in support of the families of the 1,270 Islamists murdered in a mass slaying ordered by Col. Gadhafi at Abu Salim prison in Tripoli in 1996. Most of those Islamists, seen by the Gadhafi family as the biggest threat to their regime, had come from Benghazi, and indeed the forces of Islam had long appeared to be the main opposition to the dictatorship. They dominated the rebellion.

Washington's silver-haired envoy to this mess was seen by many European diplomats I spoke to as an overly optimistic and perhaps fatefully deluded backer of a movement that they felt sure was about to collapse into violent mutiny, or to impose an even bloodier dictatorship on Libya.

So it surprised many cynics, including me, when the revolutionaries calmly handed power to an elected assembly after Mr. Gadhafi's death and defeat – and when Libyans then elected, in a fair and orderly vote, a legislature in which secular liberals commanded the largest bloc, with twice as many seats as the Islamists.

The politics of Benghazi, it turned out, were not the politics of an independent Libya. But as the country worked to rebuild its civil society, many forgot that those loud voices from the east had not been silenced – and were still not entirely with the post-revolutionary project.

Tuesday's fatal attack occurred a day before Libya's National Congress was due to elect its first Prime Minister. Although the coalition of secular liberal parties controlled by the widely respected revolutionary leader Mahmud Jibril holds a plurality of seats, the very large number of unknown independent MPs means that the outcome is far from certain.

Fawzi Abdelali, the interior minister, told reporters this month that he considers Islamists a "major force" in Libya, and a potential threat to stability, given their numbers and the fact that they remain heavily armed.

So it surprised many cynics, including me, when Libyans elected, in a fair and orderly vote, a legislature in which secular liberals commanded the largest bloc, with twice as many seats as the Islamists.

At a hearing in March before the U.S. Senate, Mr. Stevens was still an optimist, speaking of the "tremendous goodwill for the United States in Libya now." After his death, Ibrahim Dabbashi, the deputy Libyan ambassador to the U.N. said: "He used to have the friends among high officials and simple Libyan people."