With the passage of time, perhaps every phenomenon is likely to mutate and generate different copies of itself. This is precisely the case with al-Qaeda. In its third generation, one can clearly see two al-Qaeda mutants co-existing - one (al-Nusra) marginally better, the other (ISIS) much worse than the original al-Qaeda organisation.The two groups had tried for months to resolve their differences and had obviously failed. Confrontations and schisms finally culminated in an open and bloody war which left 12,000 people from both sides dead.
Abu Baker al-Baghadadi, the ISIS leader, was initially hesitant about taking part in the fighting in Syria. The Syrian Opposition groups seemed to be much better equipped and larger in numbers than his own group.
Some of his aides suggested that he set up a Jihadist front in Syria led by Syrian fighters. Abu Mohamed al-Golani came to the fore with his 40-page plan for the formation of such a Jihadist front in Syria, which came later to be known as al-Nusra Front.
Al-Baghdadi admired Golani and supplied him with funds and fighters. Later, in a statement released in April 2013, Golani himself admitted that he was delegated by Baghdadi to lead this front.
With its stakes rising high and steadily increasing its strength and popularity, al-Nusra, however, did not declare its loyalty to any party, including al-Qaeda. Baghdadi sensed al-Nusra's growing influence and power, working actively and independently in Syria. He asked Golani to disband al-Nusra Front and join the ISIS, a demand which Golani adamantly refused. He told al-Baghdadi that this would undermine the Syrian revolution.
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By April 2013, the rift between the two groups became public, when Baghdadi announced - in a recorded tape - "the merger" between al-Nusra Front and ISIS to form the so-called "Islamic State of Iraq and the Levant". Using a softer, less confrontational tone, Golani refused.
In a similar recorded tape, dated 10 April 2013, he insisted on keeping al-Nusra Front and maintaining its independence. Fearing Baghdadi's violent retribution, Golani declared his loyalty to al-Qaeda and asked Zawahiri to arbitrate between him and Baghdadi.
As al-Nusra Jihadist experiment was in line with Zawahiri's theorisation, i.e. the dispersed national versions of al-Qaeda, Golani was vindicated. The arbitration came strongly in his favour since Zawahiri adjudicated that al-Nusra remain a separate group, fighting its own independent war in Syria, and that ISIS confines its fighting to Iraq. Baghdadi rejected the verdict, claiming that the arbitration was wrong. That was a momentous event. For the first time in al-Qaeda history, the branch faulted the parent organisation and rebelled against it.
ISIS rebels vs al-Qaeda mother organisation
As soon as the Islamic State was declared, al-Nusra Front suffered a severe rift. Almost one third of its fighters, mostly foreigners ("Muhajirin" or emigrants), withdrew and joined the Islamic State in Iraq, swearing allegiance to Baghdadi as their Emir. However, a large number of Syrian fighters (the Ansar or locals) decided to stay on with al-Nusra and refused to join the new ISIS organisation.
ISIS began to storm Al-Nusra strongholds and seize its headquarters. It controlled large swathes of land and "liberated territories", precisely because the larger groups among the Syrian opposition had not yet decided to confront ISIS. Only weaker and smaller groups stood up to ISIS and were easily quashed.
A fourth generation Al-Qaeda breed, equipped with some political insight, might well embrace the "nationalistic" model, which confines Jihad strictly to the national borders of each country, and opens up to political dialogue and political participation and power sharing with fellow countrymen.
Ironically, ISIS forces were fighting the Syrian opposition groups on 39 fronts but confronting the Syrian army on only three - Aleppo and its countryside, and the eastern rural areas of Hamah.
Al-Nusra's influence diminished substantially and it lost ground in many Syrian regions, particularly in the coastal area, Aleppo and al-Raqqa. ISIS on the other hand continued to expand, preceded by its ferocious reputation for kidnapping, hostage taking and suicide bombings.
Al-Muhajirin never wavered in their loyalty to the so-called Emir of ISIS, Baghdadi. In fact, some would say, Zawahiri himself never enjoyed such strong support. However, there might be a psychological factor at play here. Baghdadi gave his mostly extremist followers a free hand in the vicious campaigns they had launched against all groups and individuals who did not follow ISIS, killing, maiming and accusing them of apostasy.
Al-Nusra and other Islamic organisations in the Syrian opposition have prohibited or severely restricted such practices. Declaring an "Islamic state" and its bona fide existence on the ground in parts of Syria and Iraq might also have fuelled the ambitions of ISIS fighters and thus strengthened their loyalty to the Emir and the ISIS Islamic Emirate.
It might be early to talk about the total annihilation of ISIS in the short run. Despite the Syrian opposition's collective campaign against it, ISIS is still a solid and tight-knit organisation with ferocious fighters. In the long run, however, the possibility is there.
The very idea behind ISIS was systematically eroded with the massive popular anger the group had faced in different parts of Syria. ISIS was in fact rejected even in the northern rural areas of Syria, where Salafi ideology is readily accepted, let alone in the big cities with their more moderate middle classes. ISIS has also overstretched itself. It has expanded way beyond its ability to control the areas it occupied or, having created too many enemies, has trouble defending itself.
ISIS fighters number no more than 7,000, compared to the joint opposition armed groups with their 220,000 active fighters on the ground across Syria today.
Beyond doubt, al-Nusra will benefit immensely from taking ISIS down. Its chances to survive, and ultimately triumph, are proportionate to al-Nusra aligning itself with other opposition forces and garnering crucial popular support and acceptance. The existence of al-Nusra as a Jihadist group and its ability to expand decisively depend on it. It is also true that there are countries in the region, inclined to support al-Nusra Front, and other opposition groups, against ISIS.
Al-Nusra's possible survival might have two contradictory implications for the al-Qaeda mother organisation. The first is that al-Nusra, the better version, could well extend the lifespan of al-Qaeda network and ideology.
The second, however, is that al-Nusra might part company with the al-Qaeda mother organisation, precisely because Zawahiri was powerless to protect it when ISIS decided to attack it. Only now, he has insisted to have no links with ISIS; add to this al-Nusra's reliance on the local indigenous factor in building its organisational structures, erecting its theoretical scaffolding, and defining the "functional" role it plays in the Syrian arena. Many Syrians who believe in the just cause of their fight against the regime, are critical of belonging to al-Qaeda.
All that could well lead to a new conception of Jihad. A fourth generation al-Qaeda, equipped with some political insight, might well embrace the "nationalistic" model, which confines Jihad strictly to the national borders of each country, and opens up to political dialogue, political participation and power-sharing with fellow countrymen. The steps al-Nusra has recently taken already point to such a transformative model.
This is part two of a two-part series. Part one was published on Wednesday, February 26.
Abdulaziz Alheis is a researcher based in Doha and editor of the forthcoming book "The Afghan Dilemma".
Hamza Mustafa is a researcher with the Arab Centre for Research and Policy Studies and author of The Syrian Revolution's Virtual Realm: Specificities, Directions and the Mechanisms for the Creation of Public Opinion, 2012.
The views expressed in this article are the authors' own and do not necessarily reflect Al Jazeera's editorial policy.