ISIS and Al-Qaeda Wage ‘Small’ Wars on Margins of Civil Strife

US-backed Syrian Democratic Forces fighters stand guard next to men waiting to be screened after being evacuated out of the last territory held by ISIS, near Baghouz, eastern Syria, Feb. 22, 2019. (AP)
US-backed Syrian Democratic Forces fighters stand guard next to men waiting to be screened after being evacuated out of the last territory held by ISIS, near Baghouz, eastern Syria, Feb. 22, 2019. (AP)
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ISIS and Al-Qaeda Wage ‘Small’ Wars on Margins of Civil Strife

US-backed Syrian Democratic Forces fighters stand guard next to men waiting to be screened after being evacuated out of the last territory held by ISIS, near Baghouz, eastern Syria, Feb. 22, 2019. (AP)
US-backed Syrian Democratic Forces fighters stand guard next to men waiting to be screened after being evacuated out of the last territory held by ISIS, near Baghouz, eastern Syria, Feb. 22, 2019. (AP)

Civil wars and strife often witness smaller wars and conflict between parties fighting in the same camp. This took place, for example, between Christian parties during the 1975-90 Lebanese civil when the Kataeb and National Liberal Party waged bloody battles for dominance. They culminated in the defeat of the Tigers Militia – the armed wing of the NLP – and establishment of the Lebanese Forces.

In Afghanistan, Mujahideen factions fought against the communist rule in Kabul and its Russian supporters. No sooner had the Mujahideen claimed victory that they turned against each other in 1992, turning Kabul into rubble. Their war only ended with the rise of the Taliban, which swallowed or nearly swallowed them up whole.

In Algeria, the 1990s saw the emergence of dozens of armed groups that fought against the rulers in order to oust and replace them with an “Islamic government.” They were battling the Algerian army, while the factions were also fighting each other in order to “unite their banner.” The infighting helped the Algerian security forces to turn the tide in their favor and defeat all of the armed groups.

The above introduction leads to the question: What sort of relationship is in store in the future between the rival ISIS and al-Qaeda organizations?

Both organizations follow the same ideology even though ISIS was formed years after al-Qaeda.

ISIS is the product of the 2003 US invasion of Iraq. Al-Qaeda, meanwhile, was born in the late 1980s in Afghanistan during a time of resistance against the Red Army and communists. In the 1990s, the Egyptian al-Jihad organization merged with al-Qaeda, leading to the establishment of the so-called Qaidat al-Jihad group, which was predominantly comprised of Egyptian members.

The rift between ISIS and al-Qaeda happened after the eruption of the Syrian civil conflict in 2011. At the time, al-Qaeda in Iraq was known as the Islamic State in Iraq. The rift was the culmination of clashes between al-Qaeda’s Iraqi branch, led by Jordan’s Abu Musab al-Zarqawi, and several Sunni factions that were fighting the American “occupiers”. These factions refused the dictates of Zarqawi, who wanted to impose the authority of his organization over all Iraqi factions.

Zarqawi’s actions prompted several Sunni groups to work with the Americans and Iraqi government instead of joining an organization that was leading the country towards sectarian civil war. The Sunni resistance, or Sahwat as they would later be known, defeated al-Qaeda, forcing it to retreat from the confrontation. Command was given to Iraqi members, while the non-Iraqis took a backseat.

Zarqawi died in 2006. He was succeeded by Abu al-Hassan al-Muhajir (Abu Ayyoub al-Masri), another foreign leader of al-Qaeda. The organization was at the time, however, identified as Iraqi and operating under the name the Islamic State in Iraq, led by Abu Omar al-Baghdadi. He would be succeeded after his killing by Abu Bakr al-Baghdadi.

When the Syrian conflict erupted from peaceful protests against the regime of president Bashar Assad in 2011, Abu Bakr al-Baghdadi was quick to dispatch Syrian Abu Mohammad al-Julani to the country. Al-Julani was a leading member of al-Qaeda and worked for al-Baghdadi as part of the Islamic State in Iraq. In Syria, he was tasked with organizing an armed movement to act against the regime.

The Syrian conflict led to the fallout between al-Baghdadi and al-Julani. Al-Baghdadi wanted al-Julani to operate under his command in Syria. In 2013, the Islamic State in Iraq transformed to become the Islamic State of Iraq and the Levant after Syrian regime forces withdrew from the border with Iraq. Al-Baghdadi then declared that the Sykes–Picot border between the neighboring countries was no more.

Al-Julani, however, rebelled against his Iraqi leader, say the latter’s supporters. Al-Baghdadi’s supports showed no mercy to their adversaries, whether they were Iraqi or Syrian government soldiers, or civilians who were viewed as apostates or infidels, or even fighters from other Islamic organizations that did not swear allegiance to the “State”.

The al-Qaeda leadership tried to avert confrontation with al-Baghdadi. It sent some of its most prominent leaders to Syria to resolve the dispute or strengthen al-Julani should efforts fail to end the rift.

The Iraqi leader, however, did not forgive the Syrian for “betraying the cause.” Al-Baghdadi believed that al-Julani turned against him when he was transferred to Syria, where he formed the al-Nusra Front as an independent branch of al-Qaeda. This branch would answer directly to the al-Qaeda command based on the Afghanistan-Pakistan border, not the Iraqi leadership.

On the ground, ISIS swallowed the Syrian al-Qaeda branch whole. Its sweep of Syria was only stopped with the beginning of the operations of the US-led international coalition against al-Baghdadi’s organization in September 2014. This allowed al-Julani to catch his breath and rebuild the al-Nusra Front. Its operations became limited to northwestern Syria, the only region where al-Baghdadi’s fighters could not expand.

Al-Julani also waged small “civil” wars against extremist Islamic groups active in areas under his control. He succeeded through force and sometimes through dialogue to eliminate the majority of armed groups that were fighting independently against the regime. The groups that managed to escape began to work directly under the Turkish army and its intelligence after their forces secured vast areas of northwestern Syria (Idlib and Latakia), its north (Aleppo) and northeast (al-Raqqa).

ISIS was defeated militarily in Syria in spring 2019 and al-Baghdadi died in a US raid in the Idlib countryside later that year. ISIS retains a few cells that are trying to regroup under the command of their new leader Abu Ibrahim al‑Hashimi al‑Qurashi, but they are still weak and do not pose a serious threat to adversaries, whether in the Syrian regime or Hayat Tahrir al-Sham, which was established as a “successor” of the al-Nusra Front.

The ISIS collapse in Syria did not spell the end of clashes between the group and al-Qaeda. ISIS affiliates across the globe have pledged allegiance to their new leader and are active in combating “infidels and apostates” in various countries, such as Yemen, Somalia and Afghanistan, and the African Sahel. ISIS media boasts of these clashes and often reports on fighting between its members and al-Qaeda in the Sahel region.

There is no doubt that these small “civil wars” between ISIS and al-Qaeda may expand or become contained. The weakness of both organizations is the factor that will determine which way the fighting will go. The weakness does not allow them to wage a largescale confrontation that would end in the victory of one over the other and the “unification of banners”. The Armed Islamic Group of Algeria tried to do this in the 1990s and failed.

Another factor is that the balance of power does not favor one party over the other as it did in the past. Under al-Baghdadi, ISIS used to boast that it was ruling a “state” due to its control over large swathes of Syria and Iraq. This is no longer the case. Al-Qaeda, meanwhile, is now no more than an armed group that does not control a “state” or even an “emirate”. It is now at the command of the “owners of the land,” such as the Taliban in Afghanistan.

Both organizations appear at an impasse, meaning the competition between them and their terrorist attacks around the globe will continue for years to come, unless their leaders agree to unite forces.



As Trump Seeks to Be a Peacemaker, Netanyahu Leaves Washington without Breakthrough on Gaza Deal

 Secretary of Defense Pete Hegseth, left, and Israeli Prime Minister Benjamin Netanyahu, right, arrive for a meeting at the Pentagon, Wednesday, July 9, 2025, in Washington. (AP)
Secretary of Defense Pete Hegseth, left, and Israeli Prime Minister Benjamin Netanyahu, right, arrive for a meeting at the Pentagon, Wednesday, July 9, 2025, in Washington. (AP)
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As Trump Seeks to Be a Peacemaker, Netanyahu Leaves Washington without Breakthrough on Gaza Deal

 Secretary of Defense Pete Hegseth, left, and Israeli Prime Minister Benjamin Netanyahu, right, arrive for a meeting at the Pentagon, Wednesday, July 9, 2025, in Washington. (AP)
Secretary of Defense Pete Hegseth, left, and Israeli Prime Minister Benjamin Netanyahu, right, arrive for a meeting at the Pentagon, Wednesday, July 9, 2025, in Washington. (AP)

Israeli Prime Minister Benjamin Netanyahu’s trip to Washington this week netted President Donald Trump another nomination for the Nobel Peace Prize he covets, but the ceasefire the US leader sought for the war in Gaza didn't emerge.

Despite Trump throwing his weight behind a push for a 60-day truce between Israel and Hamas, no breakthrough was announced during Netanyahu's visit, a disappointment for a president who wants to be known as a peacemaker and has hinged his reputation on being a dealmaker.

“He prides himself or being able to make deals, so this is another test case,” said Rachel Brandenburg, the Israel Policy Forum's Washington managing director and senior fellow.

Trump’s ability to strike a ceasefire deal in the 21-month war will reveal the boundaries of his influence with Netanyahu, especially after their recent joint strikes on Iran's nuclear facilities that both leaders touted at the White House this week.

Beyond the back-to-back meetings Trump and Netanyahu had at the White House this week, there was little public evidence of progress at a time when the Republican US president is pushing to end the fighting.

‘Closer than we’ve been,’ but challenges remain

Secretary of State Marco Rubio said Thursday that when it comes to a ceasefire in Gaza, “we’re closer than we’ve been in quite a while and we’re hopeful, but we also recognize there’s still some challenges in the way.”

Rubio, who spoke to reporters while traveling in Kuala Lumpur, Malaysia, also said that Trump “wants to see a ceasefire and we’ve invested a lot of time and energy.”

Beyond ending the bloodshed, ending the war in Gaza would give Trump more leeway to strike some of the broader agreements he seeks in the Middle East, such as expanding the Abraham Accords that started in his first term and normalizing relations with Syria’s new government.

“He wants to be the one who gets hostages home and see the war in Gaza end so he can move on to some of these bigger deals,” Brandenburg said.

Even if a truce is reached, Netanyahu has promised fighting will continue if necessary until Hamas is destroyed. The group, meanwhile, has conditioned the release of the remaining hostages on Israel's withdrawal from Gaza, a stipulation Israel has been unwilling to accept.

Trump-Netanyahu relationship sees a rebound

It’s unclear how much pressure Trump put on Netanyahu in their private talks this week. But the two leaders came into the visit seeming more aligned than ever — at least for now — fresh off the president having twice come to the Israeli leader’s assistance.

Trump made the risky move to join Israel’s attacks on Iran last month, delivering pivotal US firepower while alarming world leaders and some of Trump’s “America first” supporters. Trump also inserted himself into Israel’s domestic affairs, calling for Netanyahu’s yearslong corruption trial to be thrown out.

That’s a marked turnaround in their relationship, which had appeared somewhat strained in recent years.

Trump shocked some of his fellow Republicans and staunch supporters of Israel by publicly criticizing Netanyahu not long after Hamas attacked Israel on Oct. 7, 2023, setting off the conflict.

He said that Netanyahu “was not prepared” for the attack from Hamas and that Netanyahu had “let us down” just before the US killed top Iranian general Qassem Soleimani in 2020.

Even during his last visit to the White House earlier this year, Netanyahu seemed caught off guard when Trump announced the US would hold talks with Iran over its nuclear deal rather than embrace Netanyahu’s push for military pressure.

With their military objectives aligning for a time on Iran, the Israeli leader has worked to foster a warmer relationship.

In a video he released after the US strikes, Netanyahu spoke — in English instead of Hebrew — of the “unshakeable alliance” between their countries while repeatedly praising Trump.

“His leadership today has created a pivot of history that can help lead the Middle East and beyond to a future of prosperity and peace,” Netanyahu said.

Netanyahu tries the charm offensive on Trump

In his visit to Washington this week, the Israeli leader also showed he knows how to praise the president in a way that matters greatly to him when he unveiled a letter in front of reporters and cameras to announce he had nominated him for a Nobel Peace Prize.

Those gestures, though, may only carry him so far as Trump pushes for a deal that Netanyahu may not be able to accept.

“I think if Netanyahu stands in the way too much for too long of the sort of loftier objectives Trump has set out for himself,” Brandenburg said, “Netanyahu will be cast aside as more of a problem than an asset.”

Netanyahu, like many Israelis, believes Trump is the greatest friend they have ever had in the White House and is deeply grateful for the US strikes on Iran’s nuclear sites last month.

But the Israeli leader is also under mounting public pressure to end the war as hostages languish in captivity and more Israeli soldiers are killed in guerrilla-style attacks.

Israel’s military success against Iran has given him some political capital, but if he ends the war while leaving Hamas intact, he will have broken his repeated promise of “total victory.”

His far-right coalition partners have threatened to bolt if he does that, sparking early elections that could end his nearly unbroken 16 years in power and leave him more vulnerable to long-standing corruption charges.

That may prove too heavy a price for delivering the kind of lasting ceasefire sought by Trump and demanded by Hamas. Instead, Netanyahu, who is seen as a masterful politician by friends and foes alike, is expected to thread the needle.

In a video statement on Thursday, Netanyahu said that he would agree to a “temporary” 60-day ceasefire in return for the release of half the hostages remaining in Gaza, many of whom are believed dead, and that he would begin negotiations on ending the war.

But he conditioned any lasting ceasefire on Hamas giving up its arms – something the fighters have refused to do as long as Israel occupies parts of Gaza.

If Hamas can be disarmed through negotiations, “so much the better,” Netanyahu said. “If it is not achieved through negotiations in 60 days, we will achieve it in other ways — by using force.”