Because the political parties could not agree on a permanent constitution, they adopted a Transitional Constitution with a five-member Supreme Commission serving as head of state, a Senate indirectly elected, a popularly elected House of Representatives, and a prime minister nominated by the House and confirmed by the Commission. It was a British parliamentary system with some peculiarly Sudanese modifications, and it was meant to be temporary. What followed instead was two years of coalition governments, collapsing and reforming, while the fundamental questions about Sudan's future went unanswered. Could an Arab-identifying north coexist with a predominantly non-Arab, non-Muslim south? Could secular and religious politics share a state? Could the country develop an economy that did not depend on cotton exports and foreign aid? The first parliament did not answer any of these questions.

The people most anxious about independent Sudan in January 1956 were its southern inhabitants, who had been administered separately from the north under British rule and who feared, with good reason, that Khartoum would replace British administrators with northern Sudanese ones and proceed to remake the south in the north's image. Southern representatives in parliament concentrated on winning constitutional concessions and provincial autonomy. They were not extremists. They were not, at first, advocates of violence. Most supported a federal system. But the 1955 Torit mutiny, just before independence, had already signaled that military resistance was possible, and many in the south warned that failure to grant legal concessions would drive them to rebellion. Khartoum did not listen. Or listened, and did nothing. Over the next half-century, both of Sudan's civil wars, the one that ended in 2005 and the one that followed it, began in the same frustration the first southern parliamentarians had tried, politely, to articulate.

On November 17, 1958, the day parliament was to convene, Sudan's first military coup took place. Prime Minister Abdallah Khalil, himself a retired general, had planned it with Umma Party leaders and the army's senior generals, Ibrahim Abboud and Ahmad Abd al Wahab. The justification was the usual one: the civilian government had become corrupt, factional, unable to act. Abboud created the Supreme Council of the Armed Forces and declared that political parties only served personal ambitions and would not be reestablished under civilian rule. The regime benefited from good cotton sales in its first year and from resolving the long-standing Nile waters dispute with Egypt. But it had no vision beyond holding power, and its southern policy, ordering the mass expulsion of foreign missionaries in February 1964 and closing parliament, brought the country back to the brink of civil war.

On October 20, 1964, riot police stormed a seminar at the University of Khartoum on the Problem of the Southern Sudan. They killed three people: two students, Ahmed al-Gurashi Taha from Garrasa in the White Nile and Babiker Abdel Hafiz from Wad-Duroo in Omdurman, and a university manual laborer named Mabior from southern Sudan. Three names, three specific places. The next day, October 21, 1964, protests began in Khartoum and spread across the country. The singers Mohammed Wardi and Mohammed al-Amin, two of the great voices of twentieth-century Sudan, wrote songs that encouraged the protesters and gave the movement its anthems. Civil servants, trade unionists, teachers, students, shopkeepers all joined in. Within days, Abboud's military government collapsed. The October Revolution became one of the defining moments in modern African political history, a successful nonviolent overthrow of a military regime, and its memory has fueled every Sudanese protest movement since, including the one that ousted Omar al-Bashir in 2019.

Civilian rule returned. A second parliament sat. The same parties that had failed before tried to govern again, facing the same unanswered questions about the south, the economy, the constitution. Southern guerrillas known as the Anyanya, named after a poisonous concoction, had been fighting the Sudanese government since 1963. The civilian governments of the mid-1960s could not make peace with them and could not defeat them. Disillusion spread. Military officers began to plan. On May 25, 1969, Colonel Gaafar Nimeiry led a second coup, ending the Republic of Sudan (1956-1969) and establishing the Democratic Republic of Sudan. Nimeiry would rule for sixteen years, through war and peace and Islamization, until his own fall in 1985. But that is another story. The story of 1956-1969 is the story of a first chance at democracy that the Sudanese people seized, defended, and finally could not save, not because they did not try but because the forces arrayed against them, north and south, rich and poor, civilian and military, were too many and too contradictory to be held in one state by goodwill alone.