During al-Qaeda’s early years in the 1990s, when Osama bin Laden ran the terrorist group out of Sudan, a young Libyan man who was part of his country’s besieged diaspora of Islamists used his advanced computer skills to rise to the top of the organization long before it emerged as a global menace.

After the Libyan uprising started in early 2011, Nazih Abdul-Hamed al-Ruqai — who was detained by U.S. Special Operations forces over the weekend — was among the Islamists who flocked back home. He soon received an important assignment from al-
Qaeda leaders in Pakistan, according to a U.S. intelligence official: establish a cell for the network in his strategic North African homeland, which was reeling from a brutal civil war.

“He was tasked to create a terrorist network in Libya and involved in strategic planning between al-Qaeda and Libya,” said the official, who spoke on the condition of anonymity to discuss an intelligence assessment. The official said the order was delivered within the past year, which might help explain why the Obama administration authorized the rare and risky “rendition” carried out Saturday by U.S. commandos.

American officials have said the capture of Ruqai, who used the alias Anas al-Libi, could yield a trove of new information about the enigmatic operative, who was instrumental in the rise of al-
Qaeda and appeared to be playing a key role in its renaissance. There is relatively little public information about what he has been doing since he fled Britain in 1999.

Ruqai, 49, is being held somewhere in the Mediterranean Sea aboard the USS San Antonio, an amphibious transport dock. U.S. counterterrorism interrogators are hopeful that he will offer new insight into the recent transformation of al-Qaeda into a decentralized network that has consolidated new footholds in North Africa.

“My guess is that he will have a good deal to tell us about what has been going on in Libya and a significant amount of information to tell us about what al-Qaeda has been up to between 2001 and the present,” said Daniel Benjamin, who recently stepped down as the State Department’s coordinator for counterterrorism and is a foreign policy expert at Dartmouth College. “Possibly that will help us identify priorities and decide who else needs to be paid attention to.”

Ruqai was among the Islamists drawn to Afghan battlefields in the 1980s to fight the Soviet occupation. In the early 1990s, when bin Laden set out to plan a spectacular attack against U.S. embassies in Africa from his base in Sudan, the al-Qaeda leader tasked Ruqai with scoping out targets. The group later carried out the bombings against the embassies in Nairobi and Dar es Salaam, Tanzania, killing 224 people.

According to testimony provided in February 2001 by a former al-Qaeda member who became a U.S. government witness in a federal case in New York, Ruqai took photos of the U.S. Embassy in Nairobi and helped develop them in an apartment. Ruqai, who has been indicted in a federal terrorism case in New York, also stands accused of gathering information on potential British and Israeli targets in the Kenyan capital.

Besides being trained in surveillance, the computer engineer had skills that were deemed invaluable for an organization with growing transnational aspirations, said Ali Soufan, a former FBI agent who investigated the embassy bombings.

“He was definitely one of their smarter people,” Soufan said in an interview. “In the ’80s and ’90s, not a lot of people knew about computers.”

By the time the embassies were bombed, on Aug. 7, 1998, Ruqai was long gone from Sudan. He was among scores of Islamists who had fled to Britain after being granted political asylum there. In 1999, Scotland Yard investigators questioned Ruqai at the urging of FBI agents investigating the embassy bombings, Soufan said.

Ruqai vanished before investigators could gather enough evidence to detain him. The following year, agents searching his apartment found a guide al-Qaeda issued to its fighters, which later became known as the “Manchester Manual.” The 180-
page document was a blueprint of al-Qaeda’s philosophy and included vast tactical guidance.

Terrorism experts said Ruqai’s next steps remain something of a mystery. Some have reported that he spent time in Pakistan, Afghanistan and Iran. Abdullah al-Ruqai, one of the detainee’s sons, told the New York Times on Sunday that his family was held in Iran for four years under harsh conditions.

After returning to Libya in 2011 to join the rebellion against dictator Moammar Gaddafi, Ruqai did not appear to keep a low profile, despite a $5 million bounty being offered by the U.S. government for information leading to his capture. A United Nations sanctions report listed an address for him in the Libyan capital.

An August 2012 report by the Federal Research Division of the Library of Congress on al-Qaeda’s presence in Libya said Ruqai was “most likely involved in al-Qaeda strategic planning and coordination” between the network’s leaders in Pakistan and hard-line Islamist militias in Libya. The report said there had been “intense communications” from al-Qaeda leaders to Ruqai.

“He and others who found safe haven in the chaos that is now Libya are of great and growing concern to us,” said Rep. Adam B. Schiff (D-Calif.), a senior member of the House Intelligence Committee. “The hope is that he will not only shed light on the historic actions of the core of al-Qaeda, but can also provide actionable intelligence about Libya and surrounding countries.”

Schiff said that even if Ruqai were to be kept at sea for several weeks while intelligence officials attempt to debrief him, a prolonged detention is unlikely to weaken the pending criminal case against him, because government officials handling his interrogation would be “walled off” from the prosecution.

“I think both interests can be balanced,” the congressman said.

Craig Whitlock, Julie Tate, Greg Miller and Sari Horwitz contributed to this report.