[5] The rise of the Islamic Courts in Somalia began in the mid-1990s with the alliance of a group of Muslim legal scholars and business people led by Hassan Aweys (former leader of the AIAI) and Sharif Ahmed, with two other powerful elements: Yusuf Mohammed Siad Inda'ade the self-declared governor of Shabeellaha Hoose, and the militant Islamist group al-Itihaad al-Islamiya led by Hassan Abdullah Hersi al-Turki, forming the Islamic Courts Union.

Ethiopians feared that the Somali conflict would spill over into their territory, as Ethiopia's border is extremely porous and there are a variety of rebel groups that could cooperate with the Union of Islamic Courts.

Officially, the present United States' interest in the Horn of Africa region comprises desires for stability and peace in Somalia, including support of the establishment of a new government under the Transitional Federal Government, passage of the UN Security Council resolution to deploy an African-led peacekeeping force known as IGASOM, delivery of humanitarian aid, as well as warnings against the spread of extremist and terrorist groups in the region, including Al-Qaeda.

As part of Operation Enduring Freedom, the Combined Joint Task Force - Horn of Africa was established in Djibouti.

[15][16] The United States opposition to the formation of an Islamic Somalia led to the CIA making secret payments to aid Somali warlords in early 2006 organized under the name Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT).

The Ethiopian invasion began soon after the ICU began pushing out of the capital, with thousands Ethiopian National Defence Force (ENDF) troops being deployed around Baidoa city located in Bay region, far inside Somalia, in order to build a bridgehead for a future large scale military operation.

Local Somali officials and residents in Gedo region reported Ethiopian armored vehicles passing through the border town of Dolow and advancing 50 km inland to Luuq.

[29][30] The Ethiopian government made the decision to support these exiled warlords in order to oppose what in their view is a critical threat posed by the Islamic Courts to their administration of the Ogaden region.

The ICU walked out of talks with the TFG after 200 ENDF troops seized Wajid, taking control of the airport and landing two helicopters.

[37] Ethiopian forces under the command of Captain Hassey Aliow had crossed the Somali border into Hiraan numerous times in 2004 and 2005, and had several local allies amongst the Baadi’ade and Ujejeen clans.

The alliance with Mohammed Dheere, along with the clan-based support from the Galjeel to topple the Hawadle brought the ICU into Hiraan, conquering both Beletweyne and Buulo Barde by August 13.

Fighting quiets down in the north as Galmudug forms a buffer state between the ICU and Puntland, ending the violence between those two Barre Hiraale had been careful to avoid a confrontation with the ICU due to the fact that his chief opponent in the Juba Valley Alliance leadership, Mohamed Roble Jim’ale Gobale was pro-ICU.

Hiraale's fear was an ICU invasion in support of Mohamed Roble, which would lead to division within his own ranks due to partisan Sub-Clan loyalties within the JVA.

[44] On September 24, 2006, in order to prevent the deployment of thousands of AU troops in the country, the Courts advanced Jubaland and seized Kismayo, after Barre Hirale's Juba Valley Alliance withdrew from the town in the face of overwhelming opposition and the mutiny of several JVA factions to the ICU.

Anti-ICU protests in Kismayo sparked by a ban on the drug Khat by the organization resulted in the outbreak of violence and the imposition of a curfew.

Transitional Government and Ethiopian troops seize Burhakaba briefly from ICU-allied militias, directly violating the Khartoum agreements.

The ICU leadership consider the brief capture of Burhakaba as a violation of the peace agreement signed in Khartoum, and further talks, scheduled for the end of the month, seem less and less likely.

A televised address by Sharif Sheikh Ahmed, chairman of the Supreme Council and the most moderate and respected of the ICU leadership, wearing a military style outfit and holding an AK-47, broke the news of Jihad to Somalia.

In a much more low profile move Hassan Aweys, the Shura Council chairman, took it a step further and called for all Ethiopians, Muslim or otherwise, to rise up and overthrow the "oppressive regime of Meles Zenawi".

Religious leaders in the northern half of Galkacyo (the half controlled by Puntland) set up an Islamic Court, which the government of Puntland vows to dismantle or destroy, creating a tense situation as ICU forces head towards Galmudug-controlled South Galkacyo to protect the new Islamic Court.

Puntland's president, Adde Musa, signed a deal with the Islamic Court of Galkayo in order to stem the tide of violence that the town had experienced for over a week.

[57] On November 26, armed with over 30 "technicals", gunmen allied with the Islamic Courts have been reported to have taken full control over the town of Abudwaq, in western Galgadud region bordering Ethiopia.

[63] The Digil and Mirifle are a major clan in Somalia, with large populations throughout Bay and Bakool regions, and the shift in support weakened the government position considerably.

[64] On December 6, the United Nations Security Council approved a deployment of IGAD peacekeepers exempt from the UN arms embargo to protect Baidoa, effectively taking sides in the conflict.

On December 13, Somalia's prime minister announced Islamic Courts Union (ICU) forces were moving into positions for an attack on the last government stronghold of Baidoa in "what may now be an inevitable war".

[86] ICU commander Sheikh Ahmed Hassan Abuu Rayan stated he was positioning an unspecified number more militia troops along the border with Ethiopia in Far Libah town, Hiran region.

[91] On December 23, Ethiopian tanks and further reinforcements arrived in Daynuunay, 30 kilometres east of Baidoa; prompting ICU forces to vow all-out war despite a commitment to an EU-brokered peace.

[92] On December 24, Ethiopia admits that its troops are fighting the Islamists, after stating earlier in the week that it had only sent several hundred military advisors to Baidoa.

Also, the UIC top two commanders, defense chief Yusuf Indade and his deputy Abu Mansur were away on the Hajj pilgrimage in Mecca.

[95] After the Fall of Mogadishu to the Ethiopian and government forces on December 28, fighting continued in the Juba River valley, where the UIC retreated, establishing a new headquarters in the city of Kismayo.