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

Ayman al-Zawahri, one of al-Qaida’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.

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Al-Qaida leader Ayman al-Zawahri’s influence has waned and the group has been decimated since 9/11. But it has been years since his whereabouts were known, and many U.S. officials say the group is still a threat to the West. AP photo/2006 Al-Jazeera file

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

But Zawahri 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-Qaida’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-Qaida 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, assembled under the instruction of an al-Qaida leader approaching retirement age.

Zawahri’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-Qaida, even in Afghanistan and Pakistan, after 13 years of war.

UNFINISHED BUSINESS

Although al-Qaida’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-Qaida 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, Zawahri and Taliban chief Mohammad Omar – lost its most iconic figure three years ago in the U.S. raid on Abbottabad, Pakistan. But two out of the three, Zawahri 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-Qaida 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.

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

AL-QAIDA THREAT DIMINISHED

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-Qaida 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-Qaida,” Comey said, but its emergence reflects the extent to which affiliates have eclipsed the inner circle.”

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 doubts about leaving even a vestige of al-Qaida intact.

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-Qaida 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.

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.

ZAWAHRI’S INFLUENCE UNCLEAR

Many U.S. officials believe that Zawahri’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 Zawahri were killed, control of the terrorist network would probably shift to Yemen, the base for an al-Qaida affiliate that has sought to blow up U.S.-bound aircraft and whose leader, Nasir al-Wuhayshi, is already Zawahri’s designated successor.

U.S. officials said Zawahri is still based in Pakistan’s border region, protected by al-Qaida’s alliances with Taliban elements.

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

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, mainly advisers, 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.

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

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-Qaida’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.

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

Intelligence on al-Qaida 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.”

The most ominous question looming over the Afghan drawdown is whether al-Qaida’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-Qaida 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-Qaida 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.

The Syria-based cell is led by Mushin al-Fadhli, who is said to be one of the members of al-Qaida 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.

Zawahri’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-Qaida is down to 100 or so fighters. Most are entrenched in the northeastern provinces of Konar and Nurestan.

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

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