The War in Somalia was an armed conflict involving largely Ethiopian and Somali Transitional Federal Government (TFG) forces and Somali troops from Puntland versus the Somali Islamist umbrella group, the Islamic Court Union (ICU), and other affiliated militias for control of the country. There is a clear connection between War in Somalia (2009–) and the War of 2006. The war officially began shortly before July 20, 2006 when U.S. backed Ethiopian troops invaded Somalia to prop up the TFG in Baidoa. The TFG in Somalia invited Ethiopians to intervene, which became an "unpopular decision". Subsequently the leader of the ICU, Sheik Hassan Dahir Aweys, declared "Somalia is in a state of war, and all Somalis should take part in this struggle against Ethiopia". On December 24, Ethiopia stated it would actively combat the ICU.
Ethiopia's prime minister, Meles Zenawi, said Ethiopia entered hostilities because it faced a direct threat to its own borders. “Ethiopian defense forces were forced to enter into war to protect the sovereignty of the nation,” he said. “We are not trying to set up a government for Somalia, nor do we have an intention to meddle in Somalia's internal affairs. We have only been forced by the circumstances.”
The ICU, which controlled the coastal areas of southern Somalia, engaged in fighting with the forces of the Somali TFG, and the autonomous regional governments of Puntland and Galmudug, all of whom were backed by Ethiopian troops. The outbreak of heavy fighting began on December 20 with the Battle of Baidoa, after the lapse of a one-week deadline the ICU imposed on Ethiopia (on December 12) to withdraw from the nation. Ethiopia, however, refused to abandon its positions around the TFG interim capital at Baidoa. On December 29, after several successful battles, TFG and Ethiopian troops entered Mogadishu relatively unopposed. The UN also stated that many Arab nations including Egypt were also supporting the ICU through Eritrea. Although not announced until later, a small number of U.S. Special Forces troops accompanied Ethiopian and TFG troops after the collapse and withdrawal of the ICU to give military advice and to track suspected al-Qaida fighters. Both American support for the TFG and various Arab Nations' support for the ICU were isolated cases from the central motive of the war between the allied Ethiopian & Somali government forces and the allied ICU & Eritrean forces.
As of January 2007, Ethiopia said it would withdraw "within a few weeks" but the TFG, US and UN officials oppose Ethiopian withdrawal because it would create a "security vacuum," while the ICU has demanded immediate Ethiopian withdrawal.
The two sides had traded war declarations and gunfire on several occasions before. Eastern African countries and international observers fear the Ethiopian offensive may lead to a regional war, involving Eritrea, which has a complex relationship with Ethiopia and whom Ethiopia claims to be a supporter of the ICU.
As of January 2009, Ethiopian troops withdrew from Somalia following a two-year insurgency, which led to loss of territory and effectiveness of the TFG and a power-sharing deal between Islamists splinter group led by Sheikh Sharif Sheikh Ahmed's Alliance for the Re-liberation of Somalia (ARS) and TFG Prime Minister Nur Hassan in Djibouti. The al Shabaab who has separated from the ICU rejects the peace deal and continued to take territories including Baidoa. Another Islamist group, Ahlu Sunnah Waljama'ah, which is allied to the transitional government and supported by Ethiopia, continues to attack al Shabab and take over towns as well.
After the parliament took in 200 officials from the moderate Islamist opposition, ARS leader Sheikh Ahmed was elected TFG President on January 31, 2009. Since then, the al shabab radical Islamists have accused the new TFG President of accepting the secular transitional government and have continued the civil war since he arrived in Mogadishu at the presidential palace.