WASHINGTON — Whether it was the hunt for Osama bin Laden or secret airstrikes on Taliban forces in the badlands of Pakistan's border with Afghanistan, much of the Bush administration's war on terrorism has hinged on its relationship with general-turned-president Pervez Musharraf.
Musharraf was arguably the administration's most important ally in the fight against Islamic extremists. But when he resigned the presidency Monday, senior counter-terrorism officials in the U.S. government said there was more relief than anxiety rippling through their ranks that the drama over Musharraf's fate had ended.
Even at the height of his powers, the man who long commanded Pakistan's army had produced uneven results in countering the militant threat based in his country's northwest, said U.S. intelligence officials, all of whom requested anonymity because of the sensitivity of the relationship.
They complained that Musharraf had failed to root out elements of the Pakistani intelligence service that remain sympathetic to the Taliban, which has regained strength and appears to move easily across the border into Afghanistan to attack U.S. troops.
"From the American point of view, we wildly mis-estimated him and we wildly mis-estimated Pakistani capabilities," said Stephen Cohen of the Brookings Institution, who was visiting Pakistan this week.
American intelligence officials said they regarded Musharraf's resignation as inevitable, and hoped the civilian government that ousted him would now turn its attention to the anti-terrorism battle inside Pakistan.
"He's been done for a while," one high-ranking U.S. counter-terrorism official said of Musharraf. "Once the government gets this behind them, maybe they can focus on counter-terrorism and get back to the business of governing."
Not everyone shares that certainty.
"The civilian government is pretty divided in how it views relations with the United States," said Arif Rafiq, who edits the Pakistan Policy Blog. "Musharraf, for all his flaws, was seen as somebody able to manage Washington's demands in Pakistan. The civilian leadership is seen as all too willing to make concessions to Washington, including some that in the eyes of the security establishment are untenable."
In the last seven years, the CIA secured a series of agreements with Musharraf that allowed pilotless Predator aircraft to fly over Pakistan's tribal regions in search of Al Qaeda and Taliban operatives. Musharraf also permitted a major presence of CIA agents and occasional insertions of U.S. special forces in the region.
American officials said those agreements are open-ended and unlikely to be affected by Musharraf's resignation, largely because the U.S. has shored up relations with other key officials, such as Gen. Ashfaq Kayani, who replaced Musharraf as head of the army last year.
Kayani's relations with U.S. military officials date to 1988, when he attended the U.S. Army's Command and General Staff College at Ft. Leavenworth, Kan., which has a prestigious program for future military leaders.
The CIA also has long-standing ties to Kayani, who was the head of Pakistan's powerful Inter-Services Intelligence agency from 2004 to 2007, when it was largely dependent on U.S. support.
U.S. officials said the close ties to Kayani and the new relationships the U.S. is trying to forge with other top figures in the new Pakistani government, such as Prime Minister Yusaf Raza Gillani, who was welcomed to the White House last month, should take any sting out of Musharraf's departure.
"I just don't think that one person, especially given the condition he has been operating in for some time, makes that much difference," said one senior U.S. intelligence official.
U.S. officials say their immediate task is to press Pakistani security forces to take a more aggressive stand along the border region known as the Federally Administered Tribal Areas, used by extremists to attack Western troops in Afghanistan. Eventually, they hope to encourage the Pakistanis to apply some of the counterinsurgency lessons the U.S. learned in Iraq to their own lawless areas.
"We are in the post-Musharraf age," said a senior military official, who also requested anonymity. "That is an opportunity, not a liability. But it comes at a difficult time."
Last week, Ted Gistaro, the U.S. national intelligence officer for transnational threats, warned that Al Qaeda had "strengthened its safe haven in Pakistan's Federally Administered Tribal Areas by deepening its alliances with Pakistani militants," and said it "now has many of the operational and organizational advantages it once enjoyed across the border in Afghanistan, albeit on a smaller and less secure scale."
Critics said the revival of the extremist threat signals the failure of the Bush-Musharraf partnership.
"It ends an era marked by great cooperation but unfulfilled expectations," said analyst Bruce Hoffman of Georgetown University.
Staff writers Laura King in Islamabad, Pakistan, and Julian E. Barnes in Washington contributed to this report.