The September 11 attack that claimed the life of the US ambassador to Libya, Christopher Stevens, and three other Americans disrupted a major CIA operation in the North African country.

According to the New York Times, at least half of the nearly two dozen US personnel evacuated from the eastern Libyan city of Benghazi following the fatal attack on the US consulate and a secret “annex” were “CIA operatives and contractors.”

“It’s a catastrophic intelligence loss,” a US official who had been stationed in Libya told the Times. “We got our eyes poked out.”

The Times report describes the mission of the CIA station in Benghazi as one of “conducting surveillance and collecting information on an array of armed militant groups in and around the city,” including Ansar al-Sharia, an Islamist militia that has been linked by some to the September 11 attack, and Al Qaeda in the Islamic Maghreb, or AQIM.

It further states that the CIA “began building a meaningful but covert presence in Benghazi” within months of the February 2011 revolt in Benghazi that seized the city from forces loyal to the government of Colonel Muammar Gaddafi. Stevens himself was sent into the city in April of that year as the American envoy to the so-called “rebels” organized in the Benghazi-based National Transitional Council (NTC).

What the Times omits from its account of CIA activities in Benghazi, however, is that the agency was not merely conducting covert surveillance on the Islamists based in eastern Libya, but providing them with direct aid and coordinating their operations with those of the NATO air war launched to bring down the Gaddafi regime. In this sense, the September 11 attack that killed Stevens and the three other Americans was very much a case of the chickens coming home to roost.

There is every reason to believe that the robust CIA presence in Benghazi after Gaddafi’s fall also involved more than just surveillance. Libyan Islamists make up the largest single component of the “foreign fighters” who are playing an ever more dominant role in the US-backed sectarian civil war being waged in Syria with the aim of toppling the government of President Bashar al-Assad. According to some estimates, they comprise anywhere from 1,200 to 1,500 of approximately 3,500 fighters who have been infiltrated into Syria from as far away as Chechnya and Pakistan.

The CIA has also set up a center on the border between Turkey and Syria to oversee the funneling of arms, materiel, money and fighters into the Syrian civil war. Given the relationship established between the US agency and the Libyan Islamist militias during the US-NATO war to topple Gaddafi, it seems highly probable that the departure of such elements from eastern Libya and their infiltration into Syria would be coordinated by CIA personnel on both ends.

The government installed by the US-NATO war in the Libyan capital of Tripoli was apparently unaware of the size of the CIA presence in Benghazi, though the agency was supposedly cooperating with Libyan intelligence officials in monitoring the activities of the Islamists.

According to a report published September 21 in the Wall Street Journal, the attempt by Libyan government forces to coordinate a response to the militia assault on the US consulate and the “annex” used by the CIA was hindered by the refusal of American officials to provide the Libyans with GPS coordinates for the “annex,” which came under sustained assault and where two security contractors, former Navy Seals, were killed.

When the US and Libyan rescuers managed to evacuate some 30 Americans from the “annex” and bring them to the Benghazi airport, Libyan officials were stunned by the number of US personnel there and had to bring in a second plane to fly them all out.

“We were surprised by the numbers of Americans who were at the airport,” Libyan Deputy Prime Minister Mustafa Abushagour told the Journal. “We have no problem with intelligence sharing or gathering, but our sovereignty is also key,” he added.

In the aftermath of the attack in Benghazi, the question of security at US facilities has become a politically contested issue, with Republicans charging that the Obama administration had behaved irresponsibly in not having US military personnel protect Stevens and other personnel. They have also accused the administration of misleading the public by describing the assault on the two buildings as an outgrowth of a spontaneous demonstration over the anti-Islamic film that has triggered protests throughout the Muslim world, rather than a terrorist attack.

House Armed Services Committee Chairman Howard McKeon, a California Republican, last week declared the lack of military guards in Benghazi as “inconceivable” given an earlier attack on the Benghazi compound and other incidents of armed violence in the city.

Secretary of State Hillary Clinton responded to the criticism by insisting that local security forces and a private security company that deployed Libyan guards had provided security “of the kind that we rely on in many places around the world.”

By late last week, administration officials had begun referring to the assault as a “terrorist attack.” With the US having deployed warships, drones and a 50-member US Marine rapid reaction force to Libya, this may be preparation for military retaliation.

In Libya itself, thousands of people marched in Benghazi on Friday against the militias. Crowds laid siege to the headquarters of Ansar al-Sharia and another Islamist militia, the Rafallah Sahati brigade, leading to at least four deaths.

The demonstrations clearly expressed public anger over the sway of the Islamists over Benghazi, with participants talking of the need for “a new revolution.”

Late on Saturday, the authorities in Tripoli responded to the popular frustration. The Libyan army chief, Yusseff Mangoush, and national assembly leader Mohamed Magrief announced that “illegitimate” militias would have 48 hours to disarm and disband, or the army would use force.

What this meant was far from clear, however, as Libyan President Mohamed el-Megaref called upon Libyan protesters to leave the “legitimate” militias alone. The president demanded that the demonstrators stop attacks on militias that are “under state legitimacy, and go home.”

The spokesman for the national assembly went further. According to the Wall Street Journal, the spokesman, Omar Humidan, declared that while the militias “have wrong practices… serve their own agenda and have their own ideology… striking these militias and demanding they disband immediately will have grave consequences.”

He continued: “These are the ones that preserve security. The state has a weak army and no way it can fill any vacuum resulting in eviction of these militias… The street is upset because of the militias and their infighting. We are worried of the fallout in the absence of those militias. The state must be given time.”

The militias in Benghazi are almost all offshoots of the Libyan Islamic Fighting Group, a jihadist group that had ties to Al Qaeda and whose leaders were abducted and tortured by the CIA as part of Washington’s “global war on terror.” This is the case with Ansar al-Sharia, which is responsible for providing security at the Al Jala hospital in Benghazi, as well as the Rafallah Sahati brigade, which has also been deployed as a security force in the city, including during the national elections.

In the aftermath of last Friday’s demonstrations, the militias struck back, claiming that the popular repudiation of their policies had been stirred up by supporters of the former Gaddafi regime.

The Rafallah al-Sahati militia announced Monday that it had rounded up 113 people for alleged involvement in the protests. A leader of the group claimed that most of those detained were former members of the Gaddafi-era military or supporters of the deposed president.

Libyan state television reported Monday that on the outskirts of Benghazi the bodies of six Libyan soldiers were found shot, execution style, with their hands cuffed behind them. It was also reported that an army colonel had disappeared and was believed to have been kidnapped.

According to the Wall Street Journal: “Some media reports accused militiamen of taking revenge on Gaddafi-era veterans in the military; in contrast, a military spokesman, Ali al-Shakhli, blamed Gaddafi loyalists, saying they were trying to stir up trouble between the public and the militias.”