Twenty-five years after 9/11, the United States killed Osama bin Laden, decimated Al-Qaeda’s founding leadership, and spent two decades and trillions of dollars fighting a war in Afghanistan.
For more stories from The Media Line go to themedialine.org
Yet the network responsible for the September 11, 2001, attacks has not been eliminated.
Although Al-Qaeda’s senior leadership is marginalized and its capability and intent to conduct external operations remain unclear, the organization has survived through adaptation. It decentralized its command structure and embedded itself in regional conflicts, fragile states, and allied armed groups.
The attacks, which killed nearly 3,000 people, transformed global security and triggered the US-led “War on Terror.”
Beginning with the invasion of Afghanistan and the overthrow of the Taliban, the campaign evolved into a two-decade war that reshaped US foreign policy, military strategy, and geopolitics across the Middle East and South Asia.
US military forces severely weakened Al-Qaeda’s central leadership, culminating in the 2011 raid that killed bin Laden in Pakistan. The organization, though, was not eliminated.
It reorganized through decentralized networks and regional affiliates across Africa, the Middle East, and Asia.
US withdrawal revives concerns over terrorist groups in Afghanistan
The US withdrawal from Afghanistan in 2021 and the Taliban’s return to power revived a central post-9/11 concern: whether Afghanistan could again offer an environment in which terrorist organizations could regroup, recruit, and assist allied networks.
One enduring consequence of the war is the unresolved case against Khalid Sheikh Mohammed, whom US authorities describe as the alleged mastermind of the attacks.
Captured in Pakistan in 2003 and transferred to Guantanamo Bay in 2006, Mohammed has spent more than two decades in detention without trial. A military judge has scheduled his trial, alongside three co-defendants, to begin on June 5, 2028, nearly 27 years after 9/11.
The delay reflects the legal and political complications of the post-9/11 detention system.
Prosecutors recently declined to appeal a ruling excluding statements Mohammed made after years of Central Intelligence Agency detention and interrogation, choosing instead to preserve the 2028 trial schedule.
Recent UN assessments indicate that Al-Qaeda maintains a persistent presence in Afghanistan under Taliban rule. The UN Analytical Support and Sanctions Monitoring Team said in its August 10 report that Al-Qaeda’s status and strength in Afghanistan remained unchanged.
The report said the terrorist threat emanating from Afghanistan also remained largely unchanged and that the ability of numerous terrorist groups to operate there posed an enduring threat to neighboring countries and Central Asia.
Al-Qaeda aided TTP in insurgency against Pakistan, UN says
Al-Qaeda provided ideological guidance, training, and support to Tehrik-e Taliban Pakistan (TTP) in its insurgency against Pakistan, according to the report.
The UN report said Al-Qaeda’s official media arm, As-Sahab Media Foundation, published a statement on April 28 supporting the Taliban and, for the first time, TTP in operations against Pakistan.
Al-Qaeda in the Indian Subcontinent (AQIS) has evolved from a fragmented group into a regional terrorist entity, according to the UN assessment. The report said AQIS had established logistical and financial networks that operated through decentralized, scattered cells rather than large units.
The report said AQIS leaders remained in Kabul and had been issued Afghan identity documents, known as tazkiras, suggesting close cooperation between the Taliban and AQIS.
Alex Mishra, a Washington-area policy analyst focusing on Afghanistan, Al-Qaeda, and geopolitical alignments, told The Media Line that “25 years after 9/11, Al-Qaeda has a larger territorial presence across three continents than at any point since [its] founding.”
Mishra argued that the group’s lower profile should not be mistaken for disappearance or defeat.
Asif Durrani, Pakistan’s former special representative for Afghanistan and a former ambassador to Iran and the United Arab Emirates, offered a different assessment. He told The Media Line that “there was relatively little to discuss about Al-Qaeda,” which he described as an organization that had “lost its teeth and appeal.”
According to Durrani, the Islamic State (ISIS), also known as Daesh, has displaced Al-Qaeda as the more prominent jihadist threat. ISIS once controlled large areas of Iraq and Syria at the height of its power.
“Terrorism in its known form has lost its importance; the [term] ... ‘war on terror’ is no longer a currency in international politics,” Durrani said.
Durrani pointed to the case of Ahmed al-Sharaa, Syria’s president, noting that he was once associated with jihadist groups but, in his current political role, has gained acceptance from President Donald Trump and several European leaders.
Kamal Alam, formerly a nonresident senior fellow at the Atlantic Council and an expert on Afghan affairs, took a more cautionary view. He told The Media Line that “Al-Qaeda’s presence in Afghanistan is at its highest level since the Taliban’s return to power in 2021 and the group’s expulsion by US Special Forces.”
Alam said the killing of Al-Qaeda leader Ayman al-Zawahiri in Kabul after the Taliban takeover demonstrated the group’s continued presence in Afghanistan.
The Taliban publicly denies hosting terrorist groups, but Alam said UN agencies and independent assessments have documented the presence of Al-Qaeda, ISIS, and other regional and transnational armed groups in the country.
While describing Al-Qaeda as more decentralized and competing with ISIS for influence, he said the broader threat extends beyond the two groups and involves armed networks linked to Syria, Iraq, and Africa.
“The key concern is not the label, Al-Qaeda or ISIS, but the growing network of groups with regional and international connections,” Alam said.
Atlanta-based geopolitical analyst Erik Lehmkuhle told The Media Line that “the Taliban’s return to power had given Al-Qaeda a permissive environment to operate.”
Lehmkuhle cautioned against interpreting Al-Qaeda’s reduced visibility abroad as weakness or compliance, saying the group was pursuing “a deliberate strategy of operational patience.”
Andy Vermaut, a Brussels-based human rights activist and counterextremism expert, said the unresolved Mohammed prosecution remains one of the most serious failures of the post-9/11 system.
“A quarter-century after 9/11, the inability to try alleged mastermind Khalid Sheikh Mohammed is still a major outstanding problem,” Vermaut told The Media Line.
Vermaut said torture, including waterboarding, and the exclusion of statements obtained under coercion have undermined the prosecution and prolonged the case. He argued that the United States should have pursued a public trial under ordinary law rather than creating a system that has left the case unresolved for two decades.
Thaliban denies Afghan responsibility for 9/11
Afghan Taliban chief spokesman Zabiullah Mujahid rejected Afghan responsibility for the 9/11 attacks, saying the plotters received training, housing, and logistical backing outside Afghanistan and that no domestic infrastructure or complicity was involved.
“There was no such arrangement or infrastructure in Afghanistan at that time,” he told The Media Line.
Mujahid argued that Afghanistan had since undergone significant changes following “20 years of American aggression,” after which the Islamic Emirate and Islamic rule were established in the country.
He insisted that the government neither permits foreign armed factions to operate within its borders nor harbors foreign organizations, dismissing warnings of terrorist safe havens as foreign propaganda.
Without naming Al-Qaeda, Mujahid further claimed that such groups now have broader opportunities to live and operate in “Arab countries.” He did not identify the countries to which he was referring.