Since the fall of Bashar al-Assad after a lightning ten-day insurgent offensive in early December, the mood in Syria has in general been one of optimism, however cautious, as I saw for myself during a trip to the country in late February and early March.

Nobody denied the problems, which were obvious and daunting. The economy was uppermost in many minds. As normal as life could seem in Damascus, the power cuts afflict even upmarket establishments, and the most basic items are paid for in bundles of Syrian pounds (one US dollar is worth about 13,000 Syrian pounds). Still, it was almost encouraging that the focus was on economics.

The political transition process under the new government of Hay’at Tahrir al-Sham (HTS), an Islamist organisation once loyal to Al-Qaeda, has been halting, though the complaints were more about HTS’s poor communication leading to uncertainty than anything having gone wrong. The interim president, Ahmad al-Sharaa, has proven pragmatic. Damascenes have not been subjected to shari’a as they feared, for example. Crucially, the expected chaos and revenge killings never came to pass – until last week.

Most of the civilians on the coast massacred by troops under the HTS government’s authority since 6 March are Alawis (or Alawites), the sect from which the Assad family comes, the group in Syria that most unanimously did not share in the post-Assad optimism. The roots of this outlook run deep.

The Alawis are an esoteric sect, their doctrines formally kept secret from most of their own community. ‘Leaks’ down the centuries make it clear enough Alawi theology is a swirl of Neoplatonism, a gnostic-inflected version of the Trinity, and a reverence for the Prophet Muhammad’s cousin and son-in-law Ali as a manifestation of God – a belief that orthodox Muslims regard as plainly beyond the bounds of the faith. Incitement against Alawi heterodoxy has a long history, and under the militantly Sunni rule of the Ottomans the Alawis were marginalised and intermittently persecuted.

The rise to power in Syria of Hafez al-Assad in 1970, and the subsequent instrumentalisation of the Alawis as the backbone of the dynastic regime, above all in the army, challenged what many Sunnis saw as the laws of nature – namely, Alawi subordination. To mitigate this, Hafez drew on the Alawis long-practiced protective mechanism of taqiya (dissimulation), securing a fatwa in 1973 from Lebanon’s Shi’a hierarchy declaring Alawism a form of Islam. Hafez’s gambit failed in theological terms, with few Sunnis convinced, but it did contribute to the Alawis’ waning ability to forge an identity independent of the regime.

The blatant sectarianism of the power structure, an irritant whether Alawis were Muslims or not, provoked the first revolt against the Assad system, the one that ended under the rubble at Hama in February 1982. The major phase of the rebellion began with a massacre of Alawi cadets, separated out from the other sects by the Muslim Brotherhood, in Aleppo in June 1979. Alawis swallowed their doubts about the dangers of being identified with the regime and closed ranks after that.

Bashar took the lessons of the 1970s and 1980s to construct his strategy for survival when rebellion returned to Syria in 2011, setting out to transform the struggle from an uprising against autocracy into a sectarian civil war by deliberately radicalising the insurgency. In creating space for Sunni jihadists, Assad – and Iran, which quickly took over the regime’s security apparatus – hoped to frighten the Alawis and other minorities (and the Sunni bourgeoisie) into clinging to the regime, and to make international actors like the US wary of supporting the anti-Assad movement.

To make doubly sure of the Alawis’ loyalty, the line between the community and the regime was deliberately blurred even further by a series of regime-orchestrated massacres early in the war, using Alawi civilians, armed with knives and pistols, to murder at close quarters their Sunni neighbours. Implicated in the regime’s crimes, and with Assad’s strategy bearing fruit as Islamist groups increasingly dominated the insurgency into 2013, most Alawis felt trapped, with the lives of their families on the line, into holding fast to the security of the Assad regime.

These were the memories, grievances, and wounds in Syrians’ minds as the post-Assad period began. The Alawis have lived in dread that the Sunnis are going to attack them and perhaps expel them wholesale from Syria ever since Assad fell, and large numbers of Sunnis have indeed been waiting for a chance to, as they see it, take revenge on a population that is collectively guilty of the crimes against them and unapologetic about it. There have been kidnappings and killings of Alawis, on the coast and particularly in Homs, since the regime disintegrated, but HTS’s leadership has, to its credit, worked diligently, and quite subtly, for three months to contain the trouble.

The dam broke on 6 March after HTS troops were ambushed in the coastal town of Jableh. About 30 members of the HTS security forces were killed, many of them burned alive.

HTS issued an amnesty, allowing former regime elements (FRE) to live unmolested if they handed in their weapons and were cleared in an investigation of war crimes. This was meant to bring harmony, and avoid the optics of an active attempt to hunt the FREs down – which would have involved a massive incursion onto the coast and clashes as it arrested hundreds of Alawis – when HTS is trying to get international legitimacy. For obvious reasons, the senior criminals of the fallen regime refused to do this, but so did perhaps 5,000 lower-level Alawi soldiers because of fears of HTS.

As a result, a space opened up for the formation of resistance to the new order, spearheaded by regime remnants. One cell, the ‘Coastal Shield Forces’, is led by former Republican Guard commander Miqdad Fatiha, and another, announced on 6 March, is the ‘Military Council to Free Syria’, led by Brig.-Gen. Ghaith Dala. Operating in a sympathetic environment of terrified Alawis, the FRE cells can recruit trained young men who have retained their weapons. Since December, this milieu of nascent insurgent units and popular Alawi rejectionism has produced 46 attacks. Claims of Iranian backing for these cells are unsubstantiated, resting largely on the identifiable leaders having worked closely with Iran, which all officers did during Assad’s time.

HTS had, after invading the coast in strength during the march on Damascus in December, made a point of quickly withdrawing most of this force, especially the trouble-making foreign jihadists, and leaving a light footprint. This is what I found when I was there two weeks ago: I only saw HTS militiamen stationed around the Russian naval base in Tartus and the Russian airbase in Latakia, and at some checkpoints in the main urban centres.

This meant that when HTS called for a general mobilisation in response to what it described as a ‘coup’ attempt on 6 March, the closest troops to hand were not the more disciplined HTS cadres under Al-Sharaa’s direct control, now reflagged as ‘General Security Service’ (GSS), but the Syrian National Army (SNA), the notoriously undisciplined and predatory Turkish proxy force, and the foreign jihadists who are concentrated in Idlib. These armed groups were joined by thousands of Sunni civilians from neighbouring areas.

While it is difficult to track exactly what happened over the next few days, it is clear that the Alawi insurgents were numerous and well-coordinated. A couple of towns and some rural areas virtually fell, and the most reliable Syrian monitoring group estimates that by 10 March the insurgents had killed 172 government troops and 211 civilians, with at least nine media activists murdered in targeted assassinations.

The bigger story, though, the one that might yet derail Syria’s transition, is the massacre of 400-plus civilians by the pro-government forces and Sunni ‘volunteers’. Contrary to the misinformation – which was rampant during this episode – only four Christians were killed in the carnage, one of them by a stray bullet. One family was saved because they identified themselves as Christians to the Islamists. The Alawis were the undisguised target of the rampage, and almost its only victims.

The attackers spoke of ‘purifying’ Syria by eliminating the Alawis. Perpetrators and victims were agreed this was ‘a jihad’. In at least one case, government troops dropped unguided munitions out of a helicopter, reminiscent of Assad’s barrel bombs. The videos that will live longest in memory showed Alawi men, beaten bloody, being made to crawl around and bark like dogs, before being shot in the back of the head. That the Islamists screamed at the Alawis the whole time that they were Assadists will reinforce the Alawi perception that when HTS speaks of ‘regime remnants’ it is code for their sect.

Pro-government Islamists roved through towns and villages across the coast, day after day, shooting any Alawi they could find and left the bodies piled in the streets. Sunni civilians, meanwhile, mixed mob violence against people with theft of property, looting Alawi homes and vehicles. Al-Sharaa, as ever, said all the right things – condemning the killings, setting up an investigative committee, and vowing to punish the perpetrators. But the tapering of the pogroms after three days might have had more to do with Alawis fleeing to the mountains out of reach of the death squads, rather than any assertion of control from Damascus.

A serious show of justice might convince those western states that are considering lifting sanctions on Syria to go ahead – albeit after a ‘decent interval’. The US is a more dubious prospect, however, and any repeat atrocities could jeopardise the limited European sanctions relief already granted. This is a knotty catch-22, as money is the most obvious way Al-Sharaa could concretise the notional integration of the SNA and other unruly ex-rebels under the command-and-control of the new national army, yet their very unruliness might deny him access to the money.

Whether Syrian domestic politics can turn back from this is unclear. Al-Sharaa’s critics regard the notion that the pogrom’s perpetrators were beyond his control as too convenient by half. After all, the SNA and the foreigners are under the authority of his Ministry of Defence – as some of them attested before going about their grim work – and acted in the context of a military operation he declared. It has also become clear that GSS troops were involved in the murders. Moreover, even if the moral difference between Al-Sharaa ordering these massacres and being unable to stop them is accepted, it does little to assuage Alawi fears that their nightmares are coming true.

After a half-century of totalitarian rule by a regime that lived by divide-and-rule among the sects, an eruption such as happened after 6 March on the coast was inevitable. There is scope for optimism in it simmering down so quickly and in aspects of the popular Sunni reaction, notably the formation of a human chain to protect Alawi neighbourhoods in Homs. Alawi denunciations of the 6 March rebellion, as a cynical attempt to provoke mass-crimes against the community that make Alawi participation in the political transition impossible, give some hope we are not past the point of no return, and the public threats from one of the insurgent leaders to kill Alawis who did not join him suggest the sect as a whole has not yet decided on rejectionism. The underlying structural reality, however, is that Syria’s social fabric is in shreds, and forces embodying some of Syria’s most extreme sectarian tendencies are ascendant on all sides.

Whatever Al-Sharaa now believes, HTS has inculcated the most venomous hatred of Alawis in its members for a decade and more. The rank-and-file has not abandoned these views, other ex-rebels share much of this outlook, and sectarian sentiment runs strong among the broader Sunni masses. The Alawis, accustomed by historical memories (accurate and not) to see Sunnis as threatening, are as steeped in the sectarian bloodshed of the last decade as everyone else, and have been radicalised by it. If young Alawi men throw in their lot with the persisting regime remnants, it may be out of fear and in perceived self-defence. But if a cycle of violence begins it will be difficult to stop, not least because of the opportunities it will give spoilers like Iran and Russia. We will only know in retrospect if last week was a blip or the crossing of a Rubicon.