[On the rare occasions that Mr. Trump has spoken of Afghanistan, it has usually been to state his desire to withdraw from what he has termed “a total and complete disaster.” But the most prominent member of the national security team he is assembling, Michael T. Flynn, a retired lieutenant general and former chief of the Defense Intelligence Agency who spent years focusing on the Afghan conflict, has been outspoken about his concerns that the chaos in Afghanistan may again directly threaten the United States.]
By Mujib Mashal and Eric Schmitt
KABUL, Afghanistan — Afghanistan’s security crisis is fueling new opportunities for Al Qaeda, the Islamic State and other extremist groups, Afghan and American officials say, voicing concerns that the original American mission in the country — removing its use as a terrorist haven — is at risk.
As intense Taliban offensives have taken large portions of territory out of the Afghan government’s hands, those spaces have become the stage for a resurgence of regional and international militant groups. That is despite the extended presence of nearly 10,000 American troops in the country, tasked with performing counterterrorism operations and supporting the Afghan forces that are bearing the brunt of the fighting.
Gen. Joseph L. Votel, the chief of the United States Central Command, said the Afghan government now controls only about 60 percent of the country, the Taliban hold sway over about 10 percent, and the remainder is contested. Which group or groups fill those voids of increasing ungoverned territory in Afghanistan “is something we’ll have to contend with,” he said.
“We have to be concerned about this — about the Taliban pulling together and cooperating and collaborating with other terrorist organizations,” General Votel said at a security forum in Washington this week.
Over all, Western and Afghan officials estimate that about 40,000 to 45,000 militants are active across Afghanistan. The Taliban are estimated at about 30,000 fighters, some of them seasonal. But the rest are foreign militants of different — and often fluid — allegiances, at times competing but mostly on the same side against the Afghan government and its American allies.
“Of the 98 U.S.- or U.N.-designated terrorist organizations around the globe, 20 of them are in the Af-Pak region,” Gen. John W. Nicholson, the commander of American and NATO forces in Afghanistan, said recently. “This is the highest concentration of the numbers of different groups in any area in the world.”
It is that situation that President-elect Donald J. Trump and his new security team will inherit.
On the rare occasions that Mr. Trump has spoken of Afghanistan, it has usually been to state his desire to withdraw from what he has termed “a total and complete disaster.” But the most prominent member of the national security team he is assembling, Michael T. Flynn, a retired lieutenant general and former chief of the Defense Intelligence Agency who spent years focusing on the Afghan conflict, has been outspoken about his concerns that the chaos in Afghanistan may again directly threaten the United States.
“What we have to continue to do for that entire region is to reinstill confidence that we actually can help them,” General Flynn said this year. “We cannot leave this region to the likes of these multiple terrorist organizations. There is too much at stake.”
How that debate will play out in the new administration has become a central question among Afghan officials here.
The immediate existential threat to the Afghan government has been a resurgent Taliban, which officials say have been killing 30 to 50 members of the security forces each day in recent months. The insurgents are directly threatening important provincial capitals and have again made important roadways hazardous or impassable to government forces.
The Taliban, whose leadership is mostly taking shelter in Pakistan, insist that they are focused only on regaining power within Afghanistan. And some Russian officials, including the special envoy to Afghanistan, Zamir Kabulov, have openly acknowledged maintaining some contact with the Taliban as a possible hedge against other militant groups if the government fails, though the officials insist that has not extended to aiding the insurgency.
Still, the insurgency’s recent success is directly threatening the Afghan government’s stability, and it is creating a territorial vacuum that other groups are trying to exploit.
An increasing focus of the United States counterterrorism operation has been the local affiliate of the Islamic State, which calls itself the Islamic State in the Khorasan, an ancient name for this region.
After heavy losses over the past year to American airstrikes and Afghan ground operations, the Islamic State cell is estimated at no more than a thousand fighters, most of them former members of the Pakistani Taliban from the tribal areas, according to a senior American official, who spoke on the condition of anonymity to discuss intelligence.
Nevertheless, they have proved to be a resilient force that has maintained a hold on several districts in eastern Nangarhar Province, and they continue to have contacts, for guidance and funding, with the Islamic State’s central command in Syria and Iraq, officials say.
The Islamic State militants have also taken a more active role in staging terrorist attacks. American intelligence agencies say that the group has carried out as many as seven mass-casualty attacks in Afghanistan since midsummer, including suicide bombings.
The Islamic State affiliate here has largely been seen as a competitor with the Taliban, who have publicly criticized the group and battled it around its main stronghold in the east.
But two senior Afghan officials, speaking on the condition of anonymity to discuss new intelligence, said the idea that the Taliban have been fighting the Islamic State was not an absolute fact, but rather varied across the country. While the Taliban have been waging a bloody turf war with Islamic State in the east, they have been cooperating with elements associated with the Islamic State in the north and northeast of the country, the officials said.
The senior American official also said the Haqqani militant network, whose top leader became the deputy commander of the Taliban insurgency in 2015, has actually been “more open to discussions with the Islamic State.”
Mohammed Haneef Atmar, Afghanistan’s national security adviser, warned that although the Islamic State affiliates remain a top priority in the country’s joint counterterrorism efforts with the American military in Afghanistan, most of the terrorist groups in Afghanistan share similar ideologies.
“We cannot isolate Daesh from other terrorist groups,” Mr. Atmar said, referring to the Islamic State by an Arabic acronym. “The groups all have symbiotic relationships. One group cannot stay in isolation; others provide the enabling environment.”
Second to the Islamic State is Al Qaeda, which has seen its capability largely decreased as its leaders have been targeted by United States Special Operations and drone strikes. In addition to the core of the original group, which has remained focused on terrorist attacks abroad and has a presence in Afghanistan and Pakistan, Al Qaeda has created a new branch based in those countries, Al Qaeda in the Indian Subcontinent, or AQIS, that is more regionally focused, counterterrorism officials say.
American officials estimate that both the core Al Qaeda group and the new branch number fewer than 200 total operatives in Afghanistan; Afghan officials put the number at 300 to 500.
“There is no change in the goals that Al Qaeda is pursuing, which is the destruction of the West and Muslim democracies,” Mr. Atmar said. “The difference is that they are employing other networks, such as Haqqani and Lashkar-e-Taiba. They are outsourcing some of their work, and that makes them more dangerous.”
The core of Al Qaeda in this region has lost members to defections to the Islamic State, and it has sent some fighters to Syria to compete with the Islamic State there, intelligence officials say. Several other groups affiliated with Al Qaeda in the past, particularly groups of Central Asian fighters, have shown leanings toward the Islamic State.
One fear among Afghan and Western officials is that as the Islamic State is pressured by military operations in Iraq and Syria, some of its leaders may make their way to Afghanistan, where the ungoverned space has increased and their local affiliate has established ground.
“The U.S. came to Afghanistan on the principal of not letting the country again slip into a safe haven for extremists,” said Muhammad Umer Daudzai, a former Afghan interior minister. “Nothing has changed in that threat. Al Qaeda was just a badge, just like Islamic State is. The real threat is extremism, and that has actually increased.”
Franz-Michael Mellbin, the European Union’s ambassador and special representative to Afghanistan, said that if the terrorist groups are not tackled as a whole, it will always be possible for factions of one group to switch sides or morph into others.
“Obviously, there is a threat to international security still emanating from Afghanistan,” Mr. Mellbin said. “We have seen several international groups congregating in Afghanistan. Some of them have ambitions inside Afghanistan, for example the Taliban, but majority of the groups have ambitions that go beyond Afghanistan’s borders.”
He said the new American administration has an opportunity to assess the situation and bring changes to the mission. “We don’t want to have this conversation again 15 years from now.”
Follow Mujib Mashal @MujMash and Eric Schmitt @ericschmittnyt on Twitter.
Mujib Mashal reported from Kabul, and Eric Schmitt from Washington. Fahim Abed and Jawad Sukhanyar contributed reporting from Kabul.