2nd War with Somalia - 1998-1999

In Somalia, Ethiopia continues to support groups opposed to the transitional government, and it has sent its forces into the country to track down Ethiopian dissidents and to support friendly factions. Relations with Somalia were of longer-term concern, given their ill-defined and porous border and irredentist sentiment among Somalis that produced a war in 1977–78. Oromo and to a lesser degree Somali insurgents operated from Somali territory.

About 425,000 Somali refugees and asylum seekers lived in about two-dozen countries at the end of 1999. An estimated 170,000 were refugees in Ethiopia, some 160,000 in Kenya, about 50,000 in Yemen, more than 20,000 in Djibouti, 3,000 in Tanzania, nearly 3,000 in Egypt, nearly 3,000 in Libya, about 2,000 in Eritrea, 1,000 in Uganda, and some 14,000 new asylum seekers in various European countries. An estimated 350,000 Somalis were internally displaced. Tens of thousands of Somalis also fled their homes in the southern part of the country in 1999.

Between December 1996 and January 1997 representatives of 26 Somali factions, notably excluding the SNA, held talks in Ethiopia under the auspices of Ethiopia and the Inter-Governmental Authority on Development (IGAD), a grouping of regional states. This resulted in the creation of a 41 member National Salvation Council (NSC) to act as an interim national government. Hussein Aideed condemned the NSC and insisted that he was the legitimate President. International mediation efforts continued and representatives of several Somali factions met, under Egyptian and Arab League auspices, in Cairo in March 1997. In May 1997 Ali Mahdi and Hussein Aideed signed a reconciliation agreement in Cairo. However, Aideed made it clear that he remained opposed to the Ethiopian-sponsored peace initiative. At a further conference held in Cairo, 26 Somali faction leaders, including Aideed and Ali Mahdi, signed a peace agreement in December 1997. A condition of this accord was that a national reconciliation conference be held in Baidoa in February 1998. This was never held, not least because troops loyal to Aideed remained stationed in Baidoa. Ethiopia rejected the Cairo accord on the grounds that it failed to include all members of the NSC.

Following the outbreak of the Ethiopia-Eritrea border war in 1998, concern about the activities of Eritrean-supported Somali militias prompted Ethiopia to launch cross-border raids into Somalia against faction leaders and militias loyal to Hussein Aideed. In July 1999 Ethiopian forces based in Luuq moved further into Gedo, taking Garba Harre, the Gedo capital, and Burdhubo. In August 1999 Ethiopian forces captured a number of Al-Itihaad fighters in Gedo. In September 1999 clashes took place in Garba Harre between an Ethiopian-backed SNF faction and the main SNF group. The main SNF group drove the Ethiopian- backed faction out, forcing it to retreat to Luuq.

In June 1999, after months of fighting between the RRA and SNA, the RRA backed by a 3,000 man Ethiopian force, captured Baidoa from Aideed's forces. This move was seen as part of a wider Ethiopian strategy of establishing a buffer zone inside Somalia in a line from Gedo, through Bay and Bakool to Hiran. The joint RRA-Ethiopian force conducted operations against Aideed's forces and fighters of the Oromo Liberation Front (OLF), an Ethiopian guerrilla group opposed to the Ethiopian government, whose members were being trained in Somalia by the SNA. Aideed discontinued support to the OLF after reaching an agreement with the Ethiopians in October 1999. However, Ethiopia continued to support the RRA and made armed incursions in other areas of Somalia.

From Baidoa, the RRA moved on to take the town of Bur Acaba, north-west of Mogadishu, in June 1999. The RRA leader, Colonel Hassan Mohamed Nur 'Shaatigaduud', announced the RRA's intention of liberating all Rahanweyn-populated territory between the Juba and Shabelle rivers. In September 1999 the RRA, supported by the Ethiopians and the allied Digil Salvation Army (DSA), took the town of Dinsoor in the west of Bay region. By mid-2000 the RRA had consolidated its control of Bay and Bakool regions, leaving Aideed's forces in disarray. The RRA established a regional administration for Bay region in December 1999, with a governor and senior RRA personnel taking positions in government.