The factionalism of Southern politics had continued during the 1980s, but an internal split of the SPLM/A in August 1991 proved militarily and politically disastrous, and it gave the Islamist regime in Khartoum new breathing room. Rather than exploiting this opportunity, however, the government estranged Sudan's neighbors, Egypt, Eritrea, Ethiopia, Kenya, and Uganda. This in turn gave John Garang the opportunity to establish links with those states, to regroup and to regain the military initiative. Toward the end of the decade, the military status quo ante had apparently been restored. But the political impact of violent factionalism was fundamental and has continued to this day, with disastrous results. The split forced the SPLM/A onto a new political course whereby self-determination for South Sudan became a prominent part of the Movement's platform. Meanwhile, the split itself and the end of the SPLM's Cold War attachments ensured the continuation and institutionalization of humanitarian aid to rebel-controlled areas, and in many ways this shaped South Sudan's current constellation of foreign relations.

Their darkest hour: internal factionalism in the South

On August 28, 1991, Riek Machar, Lam Akol, and Gordon Kong radioed from the small town of Nasir, in upper Nile, to all SPLM/A units: “Why John Garang must go now.” In addition to demanding a leadership change, the trio called for reform of the SPLM/A. They faulted Garang for violations of human rights and stifling internal democracy. Perhaps most controversially, they wanted the SPLM/A to fight for an independent South Sudan rather than a reformed Sudan. The dissenters came to be known as the “Nasir-faction” or “SPLM/A Nasir,” but their initial goal was to take control of the entire Movement, not to set up a rival. They needed allies from the Bahr al-Ghazal and Equatoria, where they hoped that resentment of the “Bor Dinka” would sway rebel commanders to support their coup. Although they later gained some ground in these provinces, the core area of the Nasir faction was today's Greater upper Nile region (the states of Jonglei, Upper Nile, and Unity).

The background and motivation for the “Nasir Declaration” have been hotly debated.