GIDEL, Sudan — “Sudan is so complicated,” exclaimed Joseph Aloga Jargi, a local Catholic catechist serving frontline parishes in the war-ravaged Nuba Mountains of central Sudan. He was attempting to explain to an outsider the politics of his postwar country.

A member of one of Africa's most ancient indigenous cultures, the Nuba people, and the first Catholic in his largely Muslim family, Joseph, an early target of anti-Christian violence in his village, had fled the region during the first years of the civil war, only to return in the 1990s as ambitious Church-directed relief and development programs, under the direction of the local bishop, Macram Max Gassis, got under way.

These programs, ranging from water sanitation to catechesis, were carried out in a remote area the size of the state of Maine, without roads or electricity, and under the constant threat of militia raids and aerial bombardment by Sudanese air force bombers.

Ceasefires negotiated by former U.S. Sen. John Danforth, the Bush administration's Sudan envoy, in early 2002 brought a measure of peace, and increased aid to the Nuba region, a civil war frontline since the mid-1980s.

Today, more than 20 non-government agencies operate in the Nuba Mountains.

And even greater opportunities appeared on the horizon in those waning days of 2004, my first visit to the area since the end of the fighting. The parties to Africa's longest running civil war, the insurgent Sudan People's Liberation Movement and Army, under the leadership of its longtime chairman John Garang Mabior, and the Khartoum government, led by a military junta allied with militant Islamic political parties, were applying the finishing touches to the long-awaited comprehensive peace agreement that was eventually signed Jan. 9 in the Kenyan resort town of Naivasha.

(The initial euphoria didn't last. Garang's death in a helicopter accident in July, three weeks after he had been sworn in as one of the country's vice presidents, significantly clouds the prospects for political reform in Sudan, as well as for U.S. hopes for the unity of the country.)

It was a devil's bargain, most agreed, in that the “comprehensiveness” of the peace agreement expressly excluded Darfur, a California-sized province situated west of the Nuba Mountains, in which government-armed militias continued to mount full-scale attacks against agrarian African farming communities in the southern half of the state, killing thousands and displacing millions more. This took place despite international condemnations, press coverage and the presence of Organization of African Unity peace-keeping troops.

But the peace agreement signed in Kenya — the result of more than a decade of intensive negotiations sponsored by neighboring African states and bolstered by robust American diplomacy — does provide a much-needed respite for war-weary southern Sudanese, who have borne the brunt of more than 20 years of brutal conflict with the country's northern-led government, along with the peoples of central Sudan, who brought the insurgency to northern Sudan itself.

Sudan's civil war, sparked in 1983 when then-president Jafaar Nimeiri unilaterally abrogated a previous peace agreement with southern leaders and declared shari’a (Islamic martial law) the law of the land, has resulted in the deaths of more than 2 million in southern and central Sudan, and in the displacement of more than half the population of the south.

Despite the obvious benefits of the peace, “complicated” — Aloga's word — is a fair description of the situation I encountered in central Sudan earlier this year. And the months since the peace agreement was signed have served only to deepen those complexities.

For one thing, the Khartoum government, despite public talk of peace and reconciliation, continues, in contested areas like the Nuba Mountains, to attempt to advance by stealth what its forces were unable to achieve through the long years of war — namely, to impose Arabic culture and Islamic religion on the ethnically African cultures of central and southern Sudan.

Recently, a copy of a memo hailing allegedly from an official Saudi Arabian propaganda ministry has been circulating widely among Christian groups in Sudan. The memo purportedly details proposals for the large-scale establishment of “Islamic” schools and relief organizations in rebel-held areas, at a cost of some $28 million over the next few years, in advance of the vote on the political future of southern Sudan scheduled, according to the terms of the peace agreement, for 2011.

Borrowing a page from the missionary work of the Church, this Saudi-financed humanitarian push would, it is hoped, win good will for Islam and Arabism among largely Christian and animist insurgents, and, therefore, weaken, if not eliminate the now-popular drive for countrywide political reform or, worse, from Khartoum's point of view, eventual secession of these rebel-dominated areas from the north.

In the south, where there are few northerners and an independent political infrastructure in the making, such scenarios would appear to have little chance of success, but in the religiously mixed Nuba Mountains, such a push could prove deeply divisive.

In any case, Catholic Church leaders there are taking no chances. Aware that time may not be on their side, especially if insurgent-held areas of the Nuba Mountains find themselves eventually governed from Khartoum, the Diocese of El Obeid, under whose ecclesiastical jurisdiction the Nuba Mountains falls, has launched ambitious programs to build the region's first hospital, including surgical units and medical training facilities. The diocese will also build secondary schools to complement the English-language primary school system set up during the war. Most recently, it launched plans to establish an educational radio network for the region's long-isolated and marginalized population.

More than any other single situation, locals on the ground point to the crisis in Darfur as the symbol of the shape of things to come in Sudan.

In contrast to much of the coverage in the Western media, Darfur, they say, is less an isolated atrocity than a continuation of the cultural, racial and religious war northern elites have waged against non-Arab peoples in Sudan since the country's independence in 1956.

Fearful that ethnic Africans in the province would imitate their rebellious Nuba neighbors, the Khartoum government armed local Arab militias, the aptly self-described janjaweed (devils on horseback), who first attacked civilian farmers in the 1980s. Civilian defense groups formed, which, by 2003, had become guerilla movements that, following the lead of their central and southern comrades, launched their own full-scale rebellion against Khartoum's policies.

In recent weeks, other ethnic African communities in the north have joined the fray. The Muslim Beja, based in eastern Sudan, close to the vital Port Sudan link, have issued manifestoes calling for political reform, and have tussled with government troops near Kassala. Even the Nubians (not to be confused with the Nuba), an ancient, once Christian culture in Sudan's far north, who have, perhaps, been most politically identified with the Khartoum government over the years, are drawing back from the old political consensus, based on identification with the Arab world and Islam.

As Bishop Gassis remarked in an interview earlier this year:

“When people talk about Sudan as a north-south conflict, they're wrong. The conflict is now and has always been about ethnicities: An Arab Muslim elite pitting itself against African ethnic cultures, and this throughout the country. This is made clear when we consider that while the Nuba are religiously mixed and the southerners are mainly Christian or [animists], the people of Darfur are mostly Muslim. And yet this regime fights them. Why? For racial and ethnic reasons, because they are Africans, and not Arabs. This is the heart of the whole conflict, and this is the meaning of Darfur.”

Or, as a diocesan official succinctly put it: “We are now in just a small time of peace. No one knows what the future holds.”

Gabriel Meyer is an award-winning poet, journalist and novelist. His photo-illustrated book of essays, War and Faith in Sudan, was published this past September by Eerdmans.