During mid-2006 the Islamic Courts Union (ICU) rose to power after defeating an alliance of Somali warlords, becoming the first political entity to control Mogadishu since 1991.

After several merger talks in Khartoum during the following months failed over the issues of foreign military forces in Somalia and ICU expansion out of the capital, US backed Ethiopian troops launched a full-scale invasion in late 2006 and installed the TFG under President Abdullahi Yusuf in Mogadishu.

The invasion and foreign occupation sparked a large scale insurgency that led to the rise of Al-Shabaab, resulted in an Ethiopian military withdrawal and the resignation of President Yusuf two years later.

[4] Prior to his presidency, Yusuf had been part of an Ethiopian-backed coalition of warlords that had disrupted the earlier Transitional National Government (TNG) formed in 2000.

Lewis, Yusuf's election as president and his appointment of Gedi, who had ties to Ethiopian Prime Minister Meles Zenawi, were heavily influenced by Ethiopia.

[9][10] An African Union fact finding mission to Somalia in 2005 found that the overwhelming majority of Somalis rejected troops from neighboring states entering the country.

[12][13] In March 2005, a debate on deploying foreign troops, including Ethiopian forces, to Somalia led to violence after the resolution was rejected by a vote of 156 to 55.

By insisting on the deployment of foreign troops from countries bordering Somalia, President Abdullahi Yusuf and his Prime Minister Ali Gedi disregarded the views of their cabinet, a clear majority of transitional parliament, and much of the public.

100 members of the 275-strong parliament - led by Speaker Sharif Hassan Aden - chose to move to Mogadishu, stating they would try to restore stability to the capital.

On the other hand President Abdullahi Yusuf, Prime Minister Ali Gedi and their supporters set up base in Jowhar, 90 km north of Mogadishu, citing insecurity in the capital.

[20] Despite these serious deficiencies in capacity, Günther Schlee observes that, "the idea that the TFG was the government of Somalia still persisted in legal fiction and in the ambitions of the Ethiopians.

Several TFG ministers were members of a CIA backed alliance of warlords fighting the rising Islamic Courts Union (ICU) in Mogadishu.

[23] During late July 2006, over a dozen TFG parliamentarians resigned in protest of the Ethiopian invasion,[24] and by August 2006 the government was mired in a severe internal crisis and at risk of collapse.

[26] Professor Abdi Ismail Samatar observes that the Ethiopians had complete control over the TFG headquarters and had begun arming warlords defeated by the ICU.

[31] The TFG soon began to run into increasing opposition from remnants of the Islamic Courts Union, and despite moving much of the government in January to Mogadishu, many ministers chose to remain in Baidoa.

[32] Several high ranking figures of the TFG, including ex-speaker Sharif Hassan Sheikh Aden, were fired for calling for a compromise with the ICU.

It issued directives which included a ban on public meetings, attempts to organize political campaigns and major media outlets, which were enforced by Ethiopian troops.

[38] In an effort to suppress the growing insurgency, the Ethiopian army resorted to heavy-handed military tactics, including the use of white phosphorus munitions and heavy artillery on civilian areas.

President Abdullahi Yusuf announced in a radio address that “any place from which a bullet is fired, we will bombard it, regardless of whoever is there.”[40] The presence of Ethiopian troops reinforced the authoritarian behavior of the TFG.

[42] European Union ambassador to Somalia Walter J. Lindner sent a letter to President Yusuf condemning the deliberate blockade the delivery of urgently needed humanitarian supplies relief and the bombardment of civilian areas sanctioned by the government.

This left little revenue for Puntland's own security forces and civil service employees, leaving the territory vulnerable to piracy and terrorist attacks.

[65] With the help of a small team of African Union troops, the coalition government also began a counteroffensive in February 2009 to retake control of the southern half of the country.

Ahmed also asserted that the SEMG paper had been "timed to coincide with the end of [the] transition period in order to discredit the TFG," and that the Monitoring Group was the "wrong approach for Somalia's peace and development.

[75] Per the Transitional Federal Government's (TFG) Charter,[76] Prime Minister Mohamed named a new Cabinet on 12 November 2010,[77] which has been lauded by the international community.

[81] Ahlu Sunna Waljama'a, a moderate Sufi group and an important military ally of the TFG, was also accorded the key Interior and Labour ministries.

[83] An Anti-Corruption Commission with the power to carry out formal investigations and to review government decisions and protocols was also established so as to more closely monitor all activities by public officials.

[86] According to the African Union and Prime Minister Mohamed, with increasing troop strength the pace of territorial gains is expected to greatly accelerate.

By August 2011, the government, under President Sharif Sheikh Ahmed and its AMISOM (African Union Mission in Somalia) allies managed to secure control over all of Mogadishu.

[110] Human rights organizations have documented extensive evidence of serious humanitarian law violations and widespread corruption within the Somali Transitional Federal Government.

[111] During the Ethiopian occupation of Somalia, TFG forces engaged in deliberate blockades of humanitarian assistance, employing tactics ranging from bureaucratic obstacles to physical armed roadblocks.