Al Qaeda in Syria has faced – and survived – two upheavals since 2011. Today, the organisation might be facing its third major test, and the new development brings with it a fresh challenge for Syria.

"The first challenge was the dispute with ISIL, the Iraqi organisation that founded it. The historic dispute, after the unilateral announcement by Abu Bakr Al Baghdadi in April 2013 of a merger between the two branches, saw the near crumbling of Jabhat Al Nusra. Abu Muhammad Al Jolani, its leader, rejected the merger and instead declared an oath of allegiance to Ayman Al Zawahiri, Al Qaeda’s international leader. The revelation of links to Al Qaeda also ran the risk of a backlash against it within the Syrian opposition.

Throughout 2013, however, Jabhat Al Nusra managed to recover from the shock even though it lost the majority of its foreign members to the original Iraqi patron. It utilised the rise of jihadist factions to establish itself as a vital part of the insurgency, especially in contrast to ISIL, which began to act as a third force in the conflict focusing mostly on building a government in opposition-held areas and fighting the rebels. Jabhat Al Nusra, in contrast, was closely working with the Islamic Front, a coalition of seven Islamist and jihadist groups. Jabhat Al Nusra was the Islamic Front’s plus-one, a key factor for its entrenchment in the Syrian rebellion.

By the summer of 2014, Jabhat Al Nusra had fully recovered – only to face another test. ISIL, its ideological nemesis, had risen to international notoriety after the militants captured one-third of Iraq and half of Syria. ISIL’s relentless war against the rebel forces had, in large part, led to the fracture of the Islamic Front as a coalition and weakened most of the factions that constituted the well-funded alliance. Jabhat Al Nusra lost an important ally, which enabled it to spread its options across Syria. It also lost its most important stronghold, in eastern Syria, where oil fields offered the group a major source of income.

Yet, the group weathered the storm once again. By last August, the group looked more powerful than ever. It had newly rebranded itself as Jabhat Fateh Al Sham (JFS) and claimed it no longer had links to Al Qaeda. It led a large rebel coalition into victory when the group and its allies broke a briefly-imposed siege around Aleppo. The fate of Aleppo and other parts seemed dependent on its heavy-lifting and leadership role, and many came to accept the group as indispensable. And the group wanted to use the momentum to form a merger with other factions. A series of events since then have accumulated to present a new challenge for JFS. This challenge is two-fold.

The inception of merger talks with ideologically different factions after the nominal disaffiliation from Al Qaeda led to internal dissent. Several leading members defected or suspended their membership for fear that the move represented the beginning of a slippery slope. Jund Al Aqsa, widely accused by the rebels as an ISIL front, merged into JFS in October after the former clashed with Ahrar Al Sham, which happened to be JFS’s closest ally.

So, JFS today faces a challenge from extremists who left it and others who joined its ranks. Two reports last week highlight the scope of this challenge. In an interview, Ahrar Al Sham’s leader, Ali Al Omar, candidly attacked JFS for harbouring an ISIL cell within its organisation in the form of Jund Al Aqsa. He blamed the cell for a recent string of assassinations in Idlib as the disbanded Jund Al Aqsa began to reorganise itself under the canopy of JFS. The statement is remarkable given the two group’s special relationship on the ground.

Jihadist sources told an Arabic news outlet of an intention by defectors to re-establish an Al Qaeda branch in Syria in lieu of the rebranded JFS. Hussam Al Shaafi, JFS’s official spokesman, confirmed the reported comments were made by members of the group but said they did not represent the organisation’s view. When those mostly Jordanian members left JFS, they were advised by Abu Muhammad Al Maqdisi, a Jordanian jihadist ideologue, to organise themselves and form a Syrian Taliban.

Such voices appear to be growing as the events in Syria take a new turn. The failure of the merger with other rebel groups and the weakening of the rebellion over the past few weeks may discredit the JFS leadership’s attempts to appease the rebels, which would in turn empower dissenters who opposed those attempts.

These challenges may not be fatal for JFS, but the trends are clear. Hardliners of the ISIL type are presenting a two-way challenge for JFS. Former Jund Al Aqsa members may seek a comeback especially as Idlib is emerging as a major rebel stronghold in northwestern Syria. The refusal of JFS to properly disband Jund Al Aqsa and persecute notorious members is also a source of tension with Ahrar Al Sham.

Similarly, another set of dissenters seem bent on establishing a rival organisation to JFS. According to a senior jihadist in Syria, such individuals would need one spectacular operation to make a name for themselves and attract logistical support.

Both trends point to the emergence of ISIL-type elements separate from JFS and ISIL. Such individuals will no doubt seek to exploit any emerging vacuum to build influence. Curiously, some of those elements were once part of the network of Abu Musab Al Zarqawi, the founder of ISIL. Their ambitious should therefore not be taken lightly.

Hassan Hassan is a senior fellow at the Tahrir Institute for Middle East Policy

On Twitter: @hxhassan