Even though it was not unexpected, it is still horrifying. To assume that the Sudanese revolution would manage to topple not only Omar al-Bashir but also uproot the deeply entrenched network of military and security interests behind him was always optimistic. But the success of the protests so far, and the extent and consistency of the protesters’ efforts, offered a glimmer of hope that while civilians were negotiating with the transitional military government to end military rule, their leverage in the streets was strong.

It became obvious, however, that the military regime and its associated security bodies were simply playing for time. And they have finally run out of patience. On Monday night the massacre began. The Rapid Support Forces (RSF), a paramilitary group created from the remnants of the infamous Janjaweed militia, moved against the main areas where sit-ins were occurring in Khartoum and opened fire. The troops burned the encampments, beat whoever they did not kill, and blockaded roads and hospitals so that medical support could not reach the wounded and the dying. There are reports of rape, pillage, and the bodies of the executed floating in the river Nile.

The country was then plunged into a communications blackout, with sporadic access to the internet only producing howls of bereavement and desperation as the faces of missing loved ones were circulated on social media. The body count continues to rise; the last official figure was 31, but dozens more are missing and hundreds are injured.

These are unfamiliar scenes in Khartoum. In Darfur, where the Janjaweed originated, and in other parts of Sudan from where Bashir’s government, holed up in the garrison city of Khartoum, dispatched mercenaries to violently suppress rebellion, they were commonplace. But rebellion has finally come to Khartoum, and so the Janjaweed, briefly restrained by the military and led by the deputy leader of the transitional government, were unmuzzled to do what they do best – scorched-earth suppression.

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It was always clear that the Sudanese revolution was going to be a long process of attrition. The protesters were praised for their canniness in understanding that, even though the dictator had been toppled, there would be no returning home until the military went back to the barracks. There would be no hoodwinking them with transitional periods and election promises only made in order to give the “new” military government time to bed in. But the immensity of the task has quickly become clear.

Bashir’s regime not only impoverished the country and murdered its restive and marginalised ethnic groups, it created an entire parallel security infrastructure outside the army. This grew from an informal ragtag band of village-torchers into a large organised body with its own culture, its own economy, its own grudges against the coddled elites of Khartoum – even its own foreign policy and funding. An organised body that seems to relish the opportunity to show those comfortable Khartoum dwellers – absent from the bush and desert, the wars and skirmishes of the past 20 years – who is boss. What the Sudanese revolution is reckoning with now is the very heart of Bashir’s government distilled into its essential parts: networks of patronage with too much to lose, militias grown too large to disband, and dirty deals with regional allies too important to jettison.

The RSF and the military’s foreign alliances with the powers of the Gulf represent another front against the Sudanese revolution. The RSF’s leader, General Mohamed Hamdan Dagalo, known as Hemedti, has supported the Saudi war in Yemen by providing Sudanese soldiers – some of them reported to be children – in exchange for financial assistance. The United Arab Emirates, Saudi Arabia’s partner in the coalition in Yemen, also has a strong interest in ensuring that this access to Sudan’s cannon fodder continues.

Egypt, another ally in the axis of the counter-revolution, is also wary of any civilian government in Sudan. A delegation from the Sudanese military council met with representatives of all three countries in the run-up to this week’s massacre, strongly suggesting that the plan was hatched – or at least blessed – by these allies, eager to prevent the disruption of any military support they receive from Sudan, and keen to avoid the undesirable optics of a successful civilian revolution in the region.

And so the Sudanese revolution is fighting against four governments. The international community – so interested and morally exercised by Bashir’s human rights abuses in the past that it has left Sudan hobbled by years of economic sanctions and international isolation – has now moved on. It will only issue the usual boilerplate condemnations of violence.

The Sudanese remain alone, locked in a death grip with a government that has now dropped all pretence of negotiation or compromise. Layer by layer, Bashir’s regime has been stripped back to show its true face. There is no longer any amnesty afforded to those from the right class or ethnic background, if the price for that mercy would mean the relinquishing of power. Sudan’s wars have come home to the capital.

• Nesrine Malik is a Guardian columnist