Ties Between Al-Qaeda and the Taliban... Will ISIS benefit from the Rupture?

Taliban members are seen in Kabul after the drone strike that killed Zawahiri. (Reuters)
Taliban members are seen in Kabul after the drone strike that killed Zawahiri. (Reuters)
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Ties Between Al-Qaeda and the Taliban... Will ISIS benefit from the Rupture?

Taliban members are seen in Kabul after the drone strike that killed Zawahiri. (Reuters)
Taliban members are seen in Kabul after the drone strike that killed Zawahiri. (Reuters)

After having killed Al Qaeda leader Ayman al-Zawahiri with a drone that hit the home he had been hiding in Kabul, the United States has, to a large extent, finished avenging the 9/11 attacks.

The perpetrators were killed in bloody attacks, and Osama bin Laden was then killed by Navy SEALs in May 2011 in Pakistan. Khaled Sheikh Mohammed, the “mastermind” behind the attacks, remains in Guantanamo Bay after being arrested in Pakistan years ago. Many of the other perpetrators are either rotting there with him or were killed by the US.

But what does eliminating Zawahiri mean? This article tries to answer that question.

A contentious, complicated relationship
The first questions that come to mind ask what Zawahiri was doing in Kabul and whether his being there a year after the Taliban had returned to power, after the collapse of former President Ashraf Ghani’s government and the withdrawal of US forces, meant that an Al-Qaeda's return to the Afghan capital had been sanctioned by the Taliban.

As we all know, the US withdrew from Afghanistan after concluding the Doha Agreement with the Taliban during former President Donald Trump’s term and implementing it under Joe Biden. That agreement stipulated, among other things, that the Taliban would not allow terrorist organizations to use Afghan soil to plan or carry out attacks against any other country again.

The Taliban thus indirectly admitted that Al-Qaeda had used Afghanistan as a base from which it planned and implemented 9/11 and promised not to let that happen again after having “learned from the mistakes of the past.”

Taliban leaders have discussed learning from past mistakes a lot since returning to power. However, many are skeptical about whether the movement has actually learned its lesson after losing power for 20 years because it had harbored terrorist organizations using its territory to carry out attacks on other countries.

The skeptics point out that the Taliban has promised, for example, to allow girls to go back to school but has not done so thus far.

On the other hand, some have defended it, pointing to the fact that it has treated its former enemies well after they remained in the country despite Ghani fleeing, though it did not allow them to take part in forming the new regime in Kabul.

Regardless of whether girls are allowed back to school and how defeated rivals are treated, the international community and the US are primarily concerned with whether the country will become a sanctuary for terrorists like it had been when the Taliban first ruled in the 1990s.

In fact, several reports have discussed the prospect of an Al-Qaeda return to Afghanistan, but they cannot be confirmed in light of the Taliban’s muteness on the matter. US officials confirmed that Taliban officials had visited the safehouse where Zawahiri was killed, meaning that he had been under their protection, or at least a wing of the movement. Indeed, the ties between the two were never severed, especially in the east, where the Haqqani Network operates.

That does not mean that the leaders of this Network, who have prominent positions in Kabul, were protecting the Al-Qaeda chief in Kabul.

In truth, it is difficult to answer this question conclusively given the lack of evidence to either deny or confirm this claim, just like it had been impossible to ascertain whether bin Laden had taken permission from former Taliban leader Mullah Omar before launching the 9/11 attacks.

Who will succeed Zawahiri?
When bin Laden was killed in 2011, Zawahiri was swiftly chosen to succeed him, surprising no one. He had headed the Egyptian Islamic Jihad and was right beneath bin Laden in Al-Qaeda’s chain of command. The he men had been close since living together in Khartoum before being expelled from Sudan in 1996.

Today, the picture is far murkier. Much of Al-Qaeda’s top brass were killed, especially in Pakistan, Afghanistan and Syria. Among the most prominent leaders left is Saif al-Adl, an Egyptian Al-Qaeda official who had lived in Iran after he fled Afghanistan following the US invasion in 2001 and maintains ties with the Revolutionary Guards.

Nonetheless, Al-Qaeda might choose someone else, a figure who moved to Afghanistan to live under the new regime of the Taliban, as Zawahiri had done. Such a decision would allow it to avoid choosing someone totally controlled by Iranian intelligence like Saif al-Adl, if he indeed remains in Iran like others that it has harbored within the framework of deals it has concluded with Al-Qaeda.

Regardless of who becomes the next leader, Al-Qaeda has become a decentralized organization with no central command like that led by bin Laden in the 90s. The US war on terror forced Al-Qaeda to adapt and decentralize, and its various branches, from Yemen, to Africa to Syria, have operated independently of Zawahiri and the central command for years. This is not likely to change.

What about ISIS?
Al-Qaeda’s primary competitor, ISIS, has hit its rival hard over the past few years. Today, however, ISIS seems far worse off than Al-Qaeda. It lost its so-called state in Syria and Iraq, and it has become nothing more than dispersed small cells that launch attacks against Iraqi forces, Kurdish forces east of the Euphrates, and Syrian regime forces west of the Euphrates.

In Libya, where ISIS established an “Emirate,” it has been exterminated, with only a few cells operating in the south left. The same is true for their presence in Sinai after the Egyptian army launched a campaign against it for years. Its leader in the Sahel was killed only a few months after his most prominent competitor, the leader of Al-Qaeda in the region, was exterminated.

Its Khorasan branch remains the most active, but the major problem ISIS faces there are its clashes with the new rulers of Afghanistan, the Taliban, which is hosting their rivals, Al-Qaeda!



A Week Into the Fragile Israel-Iran Peace Agreement, Here's What We Still Don't Know

People attend the funeral procession of Iranian military commanders, nuclear scientists and others killed in Israeli strikes, in Tehran, Iran, June 28, 2025. Majid Asgaripour/WANA (West Asia News Agency) via REUTERS
People attend the funeral procession of Iranian military commanders, nuclear scientists and others killed in Israeli strikes, in Tehran, Iran, June 28, 2025. Majid Asgaripour/WANA (West Asia News Agency) via REUTERS
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A Week Into the Fragile Israel-Iran Peace Agreement, Here's What We Still Don't Know

People attend the funeral procession of Iranian military commanders, nuclear scientists and others killed in Israeli strikes, in Tehran, Iran, June 28, 2025. Majid Asgaripour/WANA (West Asia News Agency) via REUTERS
People attend the funeral procession of Iranian military commanders, nuclear scientists and others killed in Israeli strikes, in Tehran, Iran, June 28, 2025. Majid Asgaripour/WANA (West Asia News Agency) via REUTERS

It's been a week since the United States pressed Israel and Iran into a truce, ending a bloody, 12-day conflict that had set the Middle East and globe on edge.

The fragile peace, brokered by the US the day after it dropped 30,000-pound "bunker-busting" bombs on three of Iran's key nuclear sites, is holding. But much remains unsettled, The Associated Press reported.

How badly Iran’s nuclear program was set back remains murky. The prospects of renewed US-Iran peace talks are up in the air. And whether US President Donald Trump can leverage the moment to get Israeli Prime Minister Benjamin Netanyahu 's government and Hamas focused on a ceasefire and hostage deal that brings about an end to the 20-month war in Gaza remains an open question.

Here is a look at what we still don't know:

How far Iran's nuclear program has been set back Trump says three targets hit by American strikes were “obliterated.” His defense secretary said they were “destroyed.”

A preliminary report issued by the US Defense Intelligence Agency, meanwhile, said the strikes did significant damage to the Fordo, Natanz and Isfahan sites, but did not totally destroy the facilities.

Rafael Grossi, head of the International Atomic Energy Agency, said on CBS’ “Face the Nation” on Sunday that the three Iranian sites with “capabilities in terms of treatment, conversion and enrichment of uranium have been destroyed to an important degree.” But, he added, “some is still standing” and that because capabilities remain, “if they so wish, they will be able to start doing this again.” He said assessing the full damage comes down to Iran allowing inspectors access.

What future US-Iran relations might look like

After the ceasefire deal came together, Trump spoke of potentially easing decades of biting sanctions on Tehran and predicted that Iran could become a “great trading nation” if it pulled back once-and-for-all from its nuclear program.

The talk of harmony didn't last long.

Ali Khamenei, in his first public appearance after the ceasefire was announced, claimed Tehran had delivered a “slap to America’s face." Trump responded by suggesting the supreme leader own up to the fact Iran “got beat to hell. The president also said he was backing off reviewing any immediate sanction relief, because of Khamenei's heated comments.

White House officials say the US and Iran are already in early discussions about resuming negotiations that had ended after Israel began launching strikes. But Iranian Foreign Minister Abbas Araghchi says there's no agreement in place to restart talks.

It's unclear if Iran's leadership is ready to come to the table so soon after the fighting has ended — especially if Trump holds to the position that Iran must give up nuclear enrichment for even civilian use. And Trump has offered conflicting statements about his commitment to talks. “We may sign an agreement,” he said Wednesday at a NATO summit press conference. He added, “I don’t think it’s that necessary.”

What role Iran's supreme leader will play

Khamenei's age and recent diminished appearance have raised questions about the scope of his involvement in US-Iran relations and Iran's response to both American and Israeli strikes. But despite having spent the last few weeks in a bunker as threats to his life escalated, there is little indication that Khamenei does not still reign supreme over the country's massive military and governmental operations.

Khamenei has ruled three times longer than his predecessor, the late Ruhollah Khomeini, and has shaped life for the country's more than 90 million people perhaps even more dramatically.

He entrenched the system of rule by the “mullahs,” or Shiite Muslim clerics. That secured his place in the eyes of hard-liners as the unquestionable authority, below only that of God. At the same time, Khamenei built the paramilitary Revolutionary Guard into the dominant force in Iran’s military and internal politics.

How Iran might strike back Iran's retaliatory missile attacks on a US base in Qatar following the American bombardment were sloughed off by the White House as a half-hearted, face-saving measure. The US was forewarned and the salvos were easily fended off.

Yet Iran remains a persistent threat, particularly via cyberwarfare. Hackers backing Tehran have already targeted US banks, defense contractors and oil industry companies — but so far have not caused widespread disruptions to critical infrastructure or the economy.

The US Department of Homeland Security last week issued a public bulletin warning of increased Iranian cyber threats. And the US Cybersecurity and Infrastructure Security Agency, is urging organizations that operate critical infrastructure like water systems, pipelines or power plants to stay vigilant.

Whether the Israel-Iran ceasefire will hold It remains a fragile peace.

Immediately following the US strikes, Trump got on the phone with Netanyahu and told the Israeli leader not to expect further US offensive military action, according to a senior White House official who was not authorized to comment publicly about the sensitive diplomatic talks.

But even as he agreed to deal, Netanyahu made clear that Israel will strike again “if anyone in Iran tries to revive this project.”

The ceasefire deal came without any agreement from Tehran on dismantling its nuclear program. Khamenei claims the attacks “did nothing significant” to Iran's nuclear facilities.

Trump expressed confidence that Iran, at the moment, has no interest in getting its nuclear program back up. “The last thing they’re thinking about right now is enriched uranium,” Trump said.

Still, Trump says he expects Iran to open itself to international inspection to verify that it doesn’t restart its nuclear program by the International Atomic Energy Agency, the UN nuclear watchdog, or some other organization "that we respect, including ourselves.”

Whether Trump can now press Netanyahu on Gaza

The president took a big gamble with his decision to order strikes on Iran's nuclear fortress.

As a candidate, he promised to quickly end Russia's brutal war in Ukraine and the Israel-Hamas conflict in Gaza, but has failed to find a resolution to either. He also vowed to keep the US military out of foreign conflicts.

But after helping Israel with US strikes on Iran, Trump — in conversations with Netanyahu and other world leaders in recent days — has made clear he wants a deal completed soon, according to two people familiar with the private discussions and were not authorized to comment publicly.

On Friday, Trump told reporters, “We think within the next week we’re going to get a ceasefire.”

Trump didn't offer any further explanation for his optimism. But Israeli Minister for Strategic Affairs Ron Dermer is expected to be in Washington this week for talks on a Gaza ceasefire, Iran and other matters, according to an official familiar with the matter. The official spoke on condition of anonymity because they were not authorized to speak to the media.