The USC's announcement of a provisional government in February 1991 angered its allies, who maintained that they had not been consulted. Other opposition movements, particularly the SSDF, felt that the USC had slighted their long years of struggle against the Siad Barre regime, and refused to accept the legitimacy of the provisional government. The SPM and the SSDF formed a loose alliance to contest USC control of the central government and ousted USC forces from Chisimayu, Somalia's main southern city. Violent clashes throughout March threatened to return the country to civil war. Although in early April 1991, the USC and its guerrilla opponents in the south agreed to a cease-fire, this agreement broke down in the latter part of the year as fighting spread throughout those areas of Somalia under the nominal control of the the provisional government. The provisional government was continuing to hold talks on power sharing, but the prospects for long-term political stability remained uncertain.

The situation in northern Somalia was even more serious for the provisional government. The dominant SNM, whose fighters had evicted Siad Barre's forces from almost all of Woqooyi Galbeed, Togdheer, and Sanaag regions as early as October 1990, had also captured the besieged garrisons at Berbera, Burao, and Hargeysa at the end of January; they were not prepared to hand over control to the new government in Mogadishu. Like its counterparts in the south, the SNM criticized the USC's unilateral takeover of the central government, and the SNM leadership refused to participate in USC-proposed unity talks. The SNM moved to consolidate its own position by assuming responsibility for all aspects of local administration in the north. Lacking the cooperation of the SNM, the provisional government was powerless to assert its own authority in the region. The SNM's political objectives began to clarify by the end of February 1991, when the organization held a conference at which the feasibility of revoking the 1960 act of union was seriously debated.

In the weeks following Siad Barre's overthrow, the SNM considered its relations with the non-Isaaq clans of the north to be more problematic than its relations with the provisional government. The SDA, supported primarily by the Gadabursi clan, and the relatively new United Somali Front (USF), formed by members of the Iise clan, felt apprehension at the prospect of SNM control of their areas. During February there were clashes between SNM and USF fighters in Saylac and its environs. The militarily dominant SNM, although making clear that it would not tolerate armed opposition to its rule, demonstrated flexibility in working out local power-sharing arrangements with the various clans. SNM leaders sponsored public meetings throughout the north, using the common northern resentment against the southernbased central government to help defuse interclan animosities. The SNM administration persuaded the leaders of all the north's major clans to attend a conference at Burao in April 1991, at which the region's political future was debated. Delegates to the Burao conference passed several resolutions pertaining to the future independence of the north from the south and created a standing committee, carefully balanced in terms of clan representation, to draft a constitution. The delegates also called for the formation of an interim government to rule the north until multiparty elections could be held.

The Central Committee of the SNM adopted most of the resolutions of the Burao conference as party policy. Although some SNM leaders opposed secession, the Central Committee moved forward with plans for an independent state, and on May 17, 1991, announced the formation of the Republic of Somaliland. The new state's border roughly paralleled those of the former colony, British Somaliland. SNM Secretary General Abdirahmaan Ahmad Ali "Tour" was named president and Hasan Iise Jaama vice president. Ali "Tour" appointed a seventeen-member cabinet to administer the state. The SNM termed the new regime an interim government having a mandate to rule pending elections scheduled for 1993. During 1991 and 1992, the interim government established the sharia as the principal law of the new republic and chose a national flag. It promised to protect an array of liberties, including freedom of the press, free elections, and the right to form political parties, and tried, albeit unsuccessfully, to win international recognition for the Republic of Somaliland as a separate country...

The SNM-USC-SPM unification agreement failed to last after Siad Barre fled Mogadishu. On January 26, 1991, the USC formed an interim government, which the SNM refused to recognize. On May 18, 1991, the SNM declared the independence of the Republic of Somaliland. The USC interim government opposed this declaration, arguing instead for a unified Somalia. Apart from these political disagreements, fighting broke out between and within the USC and SPM. The SNM also sought to establish its control over northern Somalia by pacifying clans such as the Gadabursi and the Dulbahante. To make matters worse, guerrilla groups proliferated; by late 1991, numerous movements vied for political power, including the United Somali Front (Iise), Somali Democratic Alliance (Gadabursi), United Somali Party (Dulbahante), Somali Democratic Movement (Rahanwayn), and Somali National Front (Mareehaan). The collapse of the nation state system and the emergence of clan-based guerrilla movements and militias that became governing authorities persuaded most Western observers that national reconciliation would be a long and difficult process.

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Mogadishu could not deal effectively with the political challenge in the north because the interim government of President Mahamaad gradually lost control of central authority. Even though the interim government was dominated by the USC, this guerrilla force failed to adapt to its new position as a political party. Although the USC was primarily a Hawiye militia, it was internally divided between the two principal Hawiye clans, the Abgaal and Habar Gidir. Once in power, the clans began to argue over the distribution of political offices. Interim president Mahammad emerged as the most prominent Abgaal leader whereas Aidid emerged as the most influential Habar Gidir leader. Fighters loyal to each man clashed in the streets of Mogadishu during the summer of 1991, then engaged in open battle beginning in September. By the end of the year, the fighting had resulted in divided control of the capital. Aidid's guerrillas held southern Mogadishu, which included the port area and the international airport, and Mahammad's forces controlled the area around the presidential palace in central Mogadishu and the northern suburbs.

A United Nations-mediated cease-fire agreement that came into effect in March 1992 helped to reduce the level of fighting, but did not end all the violence. Neither Mahammad nor Aidid was prepared to compromise over political differences, and, consequently, Mogadishu remained divided. Aidid's faction of the USC comprised an estimated 10,000 guerrillas. Many of these men looted food supplies destined for famine victims and interfered with the operations of the international relief agencies. They justified their actions on the grounds that the assistance would help their enemies, the USC faction loyal to Mahammad. The proMahammad forces included an estimated 5,000 fighters. They also used food as a weapon.

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Siyaad became preoccupied with daily survival and consolidated his hold on Mogadishu. Clan-based guerrilla opposition groups multiplied rapidly, following the example of the SSDF and SNM. In January 1991, forces of the Hawiye-based United Somali Congress (USC) led a popular uprising that overthrew Siyaad and drove him to seek asylum among his own clansmen. Outside Mogadishu, all the main clans with access to the vast stores of military equipment in the country set up their own spheres of influence. In May 1991 the SNM, having secured control of the former British Somaliland northern region, declared an independent "Somaliland Republic." Government in the south had largely disintegrated and existed only at the local level in the SSDF-controlled northeast region. In Mogadishu the precipitate appointment of a USC interim government triggered a bitter feud between rival Hawiye clan factions. The forces of the two rival warlords, General Maxamed Farax Caydiid (Muhammad Farah Aydid) and Cali Mahdi Maxamed (Ali Mahdi Muhammad), tore the capital apart and battled with Siyaad's regrouped clan militia, the Somali National Front, for control of the southern coast and hinterland. This brought war and devastation to the grain-producing region between the rivers, spreading famine throughout southern Somalia. Attempts to distribute relief food were undermined by systematic looting and rake-offs by militias. In December 1992 the United States led a multinational force of more than 35,000 troops, which imposed an uneasy peace on the principal warring clans and pushed supplies into the famine-stricken areas. The military operation provided support for a unique effort at peacemaking by the United Nations. In January and March 1993, representatives of 15 Somali factions signed peace and disarmament treaties in Addis Ababa, but by June the security situation had deteriorated.