As the United States mobilized against new Islamist enemies this month, the voice of an aging adversary echoed in the distance.

Ayman al-Zawahiri, one of al-Qaeda’s founders and its leader for the past three years, released a video announcing the formation of a new affiliate in India and lamenting the turmoil being caused by the rival Islamic State in Syria.

“Oh mujahideen, unite and reject differences and discord,” he said in a pleading tone that seemed to underscore the declining relevance of al-Qaeda’s core, the
Pakistan-based group that orchestrated the Sept. 11, 2001, attacks.

But Zawahiri was silent on a far more sensitive project — the creation of a cell in Syria dedicated to plots against the United States — that once again made predictions of the demise of al-Qaeda’s core seem premature.

The Khorasan group, which was struck but not destroyed by a barrage of U.S. cruise missiles this week, came into public view like the contents of an al-Qaeda time capsule. It is led by all-but-forgotten operatives who knew Osama bin Laden before the Sept. 11 attacks and, according to U.S. officials, was assembled under the instruction of an al-Qaeda leader approaching retirement age.

Zawahiri’s involvement reflects his own unwillingness to step away from a movement that in recent years has often seemed to evolve without him. But it also underscores how much remains unfinished for the United States in the conflict with al-Qaeda, even in Afghanistan and Pakistan, after 13 years of war.

Although al-Qaeda’s leadership ranks have been depleted and the Taliban replaced with a fledgling democracy, objectives that were viewed as critical at the outset of the war have faded into the realm of afterthought.

Clusters of al-Qaeda fighters in Afghanistan and Pakistan have outlasted the U.S. combat mission scheduled to end this year. Though driven from power, the Taliban appears poised to reclaim parts of the country it once ruled.

The triumvirate of U.S.-designated high-value targets after the Sept. 11 attacks — bin Laden, Zawahiri and Taliban chief Mohammad Omar — lost its most iconic figure three years ago in the U.S. raid on Abbottabad. But two out of the three, Zawahiri and Omar, are still in place.

U.S. officials insist that the war’s objectives are undiminished. “The design of our planning is that core al-Qaeda is defeated, that the leadership is eliminated and that we have in place some blend of capabilities that can disrupt any emerging threat,” said a senior Obama administration official involved in Afghanistan strategy. He, like other officials, spoke on the condition of anonymity to discuss counterterrorism policy.

A ‘dormant’ fight?

The administration’s emerging endgame, however, is murky on how it will achieve those ends. It involves making a final push to get Zawahiri even as resources devoted to that hunt rapidly shrink, and relying on Afghanistan’s unproven security forces to prevent al-Qaeda’s return.

The war in Afghanistan is increasingly “a dormant counterterrorism fight with the hope that we’re going to get one guy,” said a second senior Obama administration official who has been involved in guiding Afghanistan strategy for nearly a decade.

U.S. counterterrorism officials said the Khorasan threat has not altered their view of how badly the group they refer to as AQSL — for al-Qaeda Senior Leadership — has been degraded.

“There is not a highly capable, functioning AQSL in the Af-Pak area,” FBI Director James B. Comey said in a briefing with reporters Thursday, three days after the U.S. assault began in Syria. Khorasan may be “the progeny of al-Qaeda,” Comey said, but its emergence reflects the extent to which affiliates have eclipsed the inner circle, whose members are now “part of that phenomenon — refugees from Afghanistan and Pakistan.”

Even so, the emergence of the Khorasan group has complicated a debate within the administration over the pending U.S. departure from Afghanistan, reinforcing the rationale for shifting resources to more pressing crisis points, including Syria, but raising concerns about the risks of leaving even a vestige of al-Qaeda intact.

Zawahiri remains elusive

The push to bring U.S. troop levels in Afghanistan down to 9,800 by year’s end is part of a much broader contraction of U.S. counterterrorism resources. The CIA has closed all but two of eight or more bases that once dotted the Pakistan border, installations that served as listening posts for the National Security Agency and that enabled CIA operatives to establish networks of informants inside Pakistan. The remaining locations are likely to be shuttered within a year, U.S. officials said.

The agency’s fleet of armed drones, which crippled al-Qaeda under a barrage of airstrikes during Obama’s first term, is likely to be removed from an airstrip in Jalalabad when it is no longer defended by U.S. forces. U.S. officials said some of the drones could be moved to another base in Afghanistan, or positioned in another nearby country, if the flights are even considered necessary beyond next year.

As in Iraq, a great deal depends on the outcome of negotiations between the United States and Afghanistan over the terms of a bilateral security agreement that will influence whether U.S. forces stay in the country, where, and for how long.

The White House declined requests by The Washington Post to examine the latest version of the document, and any language it contains on whether the United States will maintain a significant counterterrorism presence.

A senior Obama administration official said significant U.S. counterterrorism capabilities are “wired into the BSA.” Asked whether the security agreement goes into details on such issues as the CIA’s drone fleet, the official replied, “Does it discuss the length of the runways? No. But does it give us what we need? Yes.”

U.S. officials said that al-Qaeda’s core still accounts for a trickle of threats monitored by U.S. spy agencies, mostly low-level plots that the group would rely on affiliates in Yemen, North Africa, Syria and elsewhere to carry out.

Many U.S. officials believe that Zawahiri’s death would cause the terrorist network’s leadership base in Pakistan to collapse.

“The number of people who could step into his shoes is maybe zero,” Matt Olsen, director of the National Counterterrorism Center, said in an interview. If Zawahiri were killed, control of the terrorist network would probably shift to Yemen, the base for an al-Qaeda affiliate that has sought to blow up U.S.-bound aircraft and whose leader, Nasir al-Wuhayshi, is already Zawahiri’s designated successor.

U.S. officials said Zawahiri is still based in the Pakistan’s border region, protected by al-Qaeda’s tribal alliances with the Haqqani network and other Taliban elements. Speculation that he has moved to an urban area or is living in a compound like bin Laden’s is regarded with skepticism.

Rumors of the Egyptian doctor’s demise surface routinely, including speculative reporting just this month that Zawahiri had been killed in a drone strike. In reality, U.S. officials said it has been years since they had reliable intelligence on his whereabouts.

“There is not that level of granularity,” said a senior Defense Department official who oversees counterterrorism operations.

The last known opportunities to kill Zawahiri came in 2006, when the CIA carried out a drone strike in the Pakistani border village of Damadola that reportedly killed 18 villagers but missed its main target. That same year, U.S. military officials planned a Special Operations raid on a compound near Chitral where Zawahiri and other top al-Qaeda operatives were thought to be gathering at the end of the Islamic holiday Eid al-Fitr.

“We were very solid that Zawahiri was going to be there,” said a senior U.S. intelligence official involved in planning the mission. The plan called for SEAL Team 6 to descend on the targeted compound by helicopter, much as it did five years later to kill bin Laden. But the operation was scrapped, the official said, mainly out of concern that it would rupture the U.S. relationship with Pakistan.

“Since then there’s been your classic rumint, but nothing has been firm” on Zawahiri’s location, the U.S. official said, using a term for information that is picked up by spy agencies but is regarded as rumor.

Battle for resources

The administration’s exit plan in Afghanistan calls for the U.S. military footprint to continue shrinking — to 5,500 troops by the end of next year, mainly at Bagram air base, and then down to just a few hundred, operating mainly as advisers from the U.S. Embassy in Kabul, by the end of 2016.

U.S. intelligence agencies, which relied on U.S. forces for security and military bases to serve as platforms for operations, have followed a similar trajectory, including a CIA station that was the largest in the world, with roughly 1,000 operatives, analysts and support staff.

“For every five people we had” in Afghanistan, the U.S. intelligence official said, “we’re going to be down to one.”

The dismantlement has become a point of friction between officials at the White House who see the resources devoted to al-Qaeda’s core as out of proportion to the threat it poses, and others reluctant to end the campaign before its leadership is stamped out.

Among those pushing hardest to preserve the CIA’s capabilities is the head of the agency’s Counterterrorism Center — an undercover operative whose first name is Mike — who has presided over what amounts to a covert air war for much of the past decade.

“Like core al-Qaeda, there is core counter-al-Qaeda in the U.S. government,” said the senior administration official involved in Afghanistan strategy.

Since 2004, the CIA has carried out 375 drone strikes in Pakistan, killing more than 3,000 people, by some estimates. Most have been lower-level militants not considered part of al-Qaeda’s leadership cadre. The strikes have also killed dozens, if not hundreds, of civilians.

The pace of the campaign has plunged from a high of 122 strikes in 2010 to just seven so far this year. U.S. officials said the numbers are likely to continue to fall, partly because al-Qaeda’s ranks are so depleted, but also because the shrinking U.S. intelligence effort is finding fewer targets.

Critics argue the cuts have already hurt U.S. security.

Intelligence on al-Qaeda in Afghanistan and Pakistan “diminishes by the day,” said Rep. Mike Rogers (R-Mich.), chairman of the House Intelligence Committee. “You’ve already introduced a new level of risk for missing something. That’s happened.”

Can al-Qaeda rebound?

The most ominous question looming over the Afghan drawdown is whether al-Qaeda’s core has truly been damaged beyond recovery, or, as U.S. counterterrorism pressure dissipates, it could begin to rebound.

The group has recovered before, including a decade ago, during a three-year span after members fled to Pakistan but before the CIA drone campaign ramped up. In that period, al-Qaeda went from survival mode to setting in motion a 2006 plot that sought to use liquid explosives to blow up 10 airliners traveling from Britain to the United States. The scheme was disrupted but triggered sweeping airport security measures.

A more recent example is the Islamic State, which was the main target of U.S. airstrikes in Syria and Iraq this week, and emerged from the remnants of an al-Qaeda affiliate in Iraq that was seen as all but destroyed. Three years after U.S. forces left Iraq, the group now controls large parts of that country and Syria, amassing weapons and cash, beheading Western hostages and forcing the United States to resume bombing runs.

U.S. officials are still trying to determine the implications of Khorasan, a group whose name is derived from a region astride Iran and Afghanistan where al-Qaeda has barely managed to avoid extinction.

The Syria-based cell is led by Mushin al-Fadhli, who is said to be one of the members of al-Qaeda close enough to bin Laden to have been aware of the Sept. 11 plot in advance; U.S. officials said they are still trying to determine whether he was killed in an airstrike this week. But the danger Khorasan poses is more dependent on a new generation, including fighters arriving in Syria with Western passports and operatives from an al-Qaeda affiliate known for its bomb-making expertise.

Zawahiri’s circle of followers in Pakistan is thought to be down to a few dozen operatives at most. Across the border, where his organization once operated sprawling training camps, al-Qaeda is down to 100 or so fighters who have managed to evade years of drone strikes and commando raids. Most are entrenched in the northeastern provinces of Konar and Nurestan, where the Kabul government has little influence.

“They have retirement homes there. They’ve married into the families,” said Maj. Gen. Stephen J. Townsend, the top U.S. commander in eastern Afghanistan. “Al-Qaeda,” he said, “is always going to be there.”

Correction: An earlier version of this story had an incorrect rank for Maj. Gen. Stephen J. Townsend

Julie Tate contributed to this report.