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.



Career Diplomat Becomes the Face of Trump’s ‘America First’ Agenda at the UN

US Ambassador to the United Nations, Dorothy Shea (C), addresses a UN Security Council meeting called following a recent missile strike by Russia on a residential area in Ukraine, at the United Nations headquarters in New York, New York, USA, 08 April 2025. (EPA)
US Ambassador to the United Nations, Dorothy Shea (C), addresses a UN Security Council meeting called following a recent missile strike by Russia on a residential area in Ukraine, at the United Nations headquarters in New York, New York, USA, 08 April 2025. (EPA)
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Career Diplomat Becomes the Face of Trump’s ‘America First’ Agenda at the UN

US Ambassador to the United Nations, Dorothy Shea (C), addresses a UN Security Council meeting called following a recent missile strike by Russia on a residential area in Ukraine, at the United Nations headquarters in New York, New York, USA, 08 April 2025. (EPA)
US Ambassador to the United Nations, Dorothy Shea (C), addresses a UN Security Council meeting called following a recent missile strike by Russia on a residential area in Ukraine, at the United Nations headquarters in New York, New York, USA, 08 April 2025. (EPA)

The highest-ranking US representative now at the United Nations told Congress two years ago that Russia's invasion of Ukraine was "unprovoked" and "unjustified," urging UN members to condemn Moscow’s aggression and demand an end to the war.

In February, it was the same career diplomat, Dorothy Shea, who voiced the Trump administration's extraordinary decision to split with European allies and refuse to back a UN resolution blaming Russia for its invasion on the third anniversary of the war.

While it is typical for diplomats to stay on as US presidents — and their political parties — change, Shea's interim role has unexpectedly made her a face of the stunning US transition on the world stage, with President Donald Trump's "America First" approach increasingly upending the post-World War II international order.

Shea will be in place longer than expected after Trump's unusual decision last month to withdraw his nominee for UN ambassador, Rep. Elise Stefanik, from consideration because of a slim Republican House majority.

"I would say (Shea’s) position is unique. It is probably particularly unique in that because of the extraordinary change, not just from one administration to another, but really an era of US foreign policy, even when there were nuanced differences," said Phillip Reeker, the former acting assistant secretary of state for Europe. "The change in the vote that took place at the UN on the Russia-Ukraine war was really an inflection point in US policy."

A UN vote changes US messaging on Ukraine

On Feb. 24, the US joined Russia in voting against a European-backed Ukrainian resolution demanding an immediate withdrawal of Moscow's forces. A dueling US resolution noted "the tragic loss of life" and called for "a swift end to the conflict," but it didn't mention Moscow’s aggression as the Trump administration opened negotiations with Russia on a ceasefire.

"Continuing to engage in rhetorical rivalries in New York may make diplomats feel vindicated, but it will not save souls on the battlefield," Shea, 59, said at the time. "Let us prove to ourselves and to our citizens that we can come together and agree on the most basic principles. Let us show one another that the bold vision of peace that once pulled us out of hell can prevail."

The message was a shocking retreat for the US in the 193-member UN General Assembly, whose resolutions are not legally binding but are seen as a barometer of world opinion. It also reinforced the fears of some allies about what a second Trump presidency could mean for longstanding transatlantic partnerships — and whether the US could remain a bulwark against aggressors like Russia.

For Shea, it was another day at work. She has spent the last 30-plus years serving as a diplomat under both Republican and Democratic presidents — from Bill Clinton to Trump — carrying out their policies even if they were a departure from longstanding US positions.

"I don’t know what her personal views are on things. But administrations change, policies change. And your job as a diplomat is to advocate for those policies," said a former colleague and deputy US ambassador, Robert Wood, who recently retired.

The US mission to the UN declined to comment. The State Department did not immediately respond to an Associated Press request for comment.

The roots of a diplomat

Shea's work has included stints in South Africa, where she witnessed Nelson Mandela become the first democratically elected president, and Israel, where she worked on the Israeli-Palestinian peace process.

Shea grew up in the suburbs of Washington — her father a World War II veteran and her mother active in the local Japanese American friendship society. The experience of Japanese exchange students staying with her family over several summers and wanting to understand world events propelled her into international relations at the University of Virginia. After graduation, she scored a job offer with the US Foreign Service.

She worked her way up and in 2019 was tapped to be Trump's ambassador to Lebanon, where the soft-spoken diplomat made headlines for her criticism of the Hezbollah group. A Lebanese judge banned local and foreign media outlets from interviewing Shea for a year, saying her criticism of Hezbollah was seditious and a threat to social peace.

In 2023, Biden nominated Shea to become No. 2 at the UN.

The top US role at the UN — for now

It is unclear when Shea will hand off to a Senate-confirmed political appointee. Stefanik went through a confirmation hearing, but her nomination was pulled last month because her vote to advance Trump's agenda remains crucial to Republicans in the House. The GOP congresswoman was the fourth Trump nominee not to make it through the confirmation process.

Trump has made no mention of whom he would nominate to replace Stefanik and fill his last remaining Cabinet seat. Until then, Shea is at the helm at a critical moment for US foreign policy, selling big changes to dealing with both allies and adversaries and defending the administration's slashing of foreign assistance.

The White House recently proposed additional drastic cuts to the State Department, which would include eliminating funding for nearly all international organizations, such as the UN.

The proposal is highly preliminary but reflects the administration's isolationist view, which, along with funding uncertainties, poses a major challenge to the mandate and work of the UN.