By Greg Miller
Washington Post Staff Writer
Monday, March 7, 2011; 9:04 PM
In a span of weeks, popular uprisings in the Islamic world have upended counterterrorism relationships that the United States spent much of the past decade trying to build.
The turmoil has emerged as a source of concern for U.S. counterterrorism officials, scrambling partnerships that have been critical to operations against al-Qaeda, even though the long-term prospect of democratic reform in the region is seen as a potential setback to the terrorist group.
The popular revolts have led to the ouster of a stalwart counterterrorism ally in Egypt, and threatened an autocrat who has allowed the United States to use drones and special operations troops to hunt al-Qaeda operatives in Yemen.
Seemingly stable monarchies such as those in Saudi Arabia and Jordan are being forced to sharpen the focus of their intelligence and security services on internal unrest. And even one of the main U.S. adversaries in the region, Libya's Moammar Gaddafi, distrusted al-Qaeda and occasionally provided intelligence to the CIA.
"Change is scary - we're going to have to create or re-create relationships with these countries," said a senior U.S. counterterrorism official. "There's certainly reason to be concerned."
The turbulence extends beyond the Middle East and North Africa. U.S. officials have struggled to repair new ruptures in the relationship between the CIA and its counterpart in Pakistan. The agency was forced to remove its top spy from Islamabad in December, and is scrambling to free another employee from prison after he fatally shot two Pakistani men in Lahore.
"On the counterterrorism front, this has been a bad winter," said Bruce Riedel, a former CIA official and adviser to the Obama administration. "That doesn't detract from the fact that al-Qaeda has had a bad winter, too."
U.S. officials cited particular apprehension about developments in Yemen, which has served as a sanctuary for al-Qaeda's most potent affiliate, al-Qaeda in the Arabian Peninsula, or AQAP.
Yemeni President Ali Abdullah Saleh has allowed an expanded CIA and U.S. military presence in his country over the past 18 months, as well as U.S. missile strikes on suspected AQAP targets.
Since last summer, Saleh has also allowed the U.S. Joint Special Operations Command to patrol his country with armed Predator drones. All of the operations are contingent on the U.S. relationship with Saleh, who is now under mounting internal pressure to end his 32-year rule.
"Whatever focus we've maintained on al-Qaeda in the Arabian Peninsula, and insisted that Saleh maintain, will be turned because of all the other pressures he's under," the senior U.S. counterterrorism official said.
AQAP is seen by U.S. counterterrorism officials as the most immediate threat to the United States and has been linked to attacks including the attempted suicide bombing of a Detroit-bound airliner on Christmas Day in 2009.
An influential Yemeni cleric this week called for Saleh to be replaced with an Islamist government, a prospect that U.S. officials said would complicate its partnership with Yemen, if not bring it to an end.
Underscoring the stakes, Director of National Intelligence James R. Clapper Jr. testified before Congress last month that unless U.S. and Yemeni disruption efforts are ramped up further, AQAP "probably will grow stronger."
U.S. officials said they also expect Egypt to become a less enthusiastic partner, though they also cite reasons to expect a certain level of counterterrorism cooperation to endure.
Omar Suleiman, named by Hosni Mubarak as his vice president in the waning days of the regime, was for years one of the CIA's closest allies in the Middle East. As head of Egypt's intelligence service, Suleiman signed off on an array of secret programs after the Sept. 11, 2001, attacks, including Egypt's involvement in the "rendition" of terrorism suspects who subsequently claimed they were tortured after being delivered to Egyptian custody by the CIA.
Suleiman left the government along with Mubarak, and his abrupt departure could hamper current counterterrorism efforts across North Africa and the Middle East.
"Two months ago Suleiman and his Yemeni counterpart and Musa Kusa all had al-Qaeda at the top of their agenda list," Riedel said. "Now their to-do lists are very different."
Kusa was formerly head of the foreign intelligence service in Libya, a job in which he was accused of conducting terrorist plots even while cracking down on groups aligned with al-Qaeda. Libyans have traditionally had disproportionately prominent roles in al-Qaeda's leadership ranks.
U.S. officials said they have cultivated relationships with other senior officials in Egypt's intelligence services and military who are expected to stay in place. They also stressed that the United States is less dependent on Egypt than it was in the years immediately after the Sept. 11 attacks.
That is in part because al-Qaeda's composition has changed. Egyptians once dominated the organization's leadership, but there is now only one native Egyptian, Ayman al-Zawahiri, in al-Qaeda's upper ranks.
More broadly, U.S. officials are convinced that the uprisings - and the prospect that more democratic and representative governments could emerge - will do significant damage to al-Qaeda's appeal. The mass protests "have the clear potential of being really bad for al-Qaeda," the senior U.S. counterterrorism official said. "They show the Arab world: Look what we can do without using suicide bombers, without doing anything in the name of Islam."
It is harder to see a silver lining in the rapidly deteriorating U.S. relationship with Pakistan, where al-Qaeda leader Osama bin Laden and much of the organization is based. In December, U.S. officials accused Pakistan's Inter-Services Intelligence directorate (ISI) of intentionally exposing the identity of the CIA's top operative in the country, forcing the agency to remove him.
The two governments are now engaged in a high-stakes standoff over the fate of a CIA security contractor, Raymond Davis, who was arrested on Jan. 27 after fatally shooting two Pakistani men he said were trying to rob him at a traffic signal in Lahore. Pakistan has threatened to prosecute Davis for murder, ignoring U.S. assertions that he is protected by diplomatic immunity.
The CIA has dramatically reduced the number of drone strikes it has carried out since Davis's arrest, perhaps seeking to avoid further provoking anti-U.S. sentiment in Pakistan.
CIA spokesman George Little said that counterterrorism work has continued despite the frictions. "The agency's ties to ISI have been strong over the years, and when there are issues to sort out, we work through them," he said.