On December 27, 2006, after a brief skirmish earlier in the day at the Battle of Jowhar, the leaders of the ICU, including Sheiks Hassan Dahir Aweys, Sharif Sheikh Ahmed and Abdirahman Janaqow resigned in a capitulation recognizing the new state of affairs in Somalia.
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On January 10, a report by Somali presidential chief of staff, Abdirizak Hassan stated the US airstrikes had killed Al Qaeda member Fazul Abdullah Mohammed, and leaders of the Islamic Courts Union including Abduallahi Moalim Ali (former chief of security for Mogadishu), Abdirahman Janaqow, and a third unidentified person.
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When Ahmed was otherwise indisposed (visiting a foreign country, ill, etc.) Sheikh Abdirahman Janaqow was the Acting Chairman.
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Abdirahman Janaqow survived those attacks and is currently the Justice Minister in his friend Sheikh Sharif Sheikh Ahmed's TFG government.
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It was created in September 2007, when members of the Islamic Courts Union and Somali opposition leaders met in Asmara, the capital of Eritrea, and united to oppose Somalia's Transitional Federal Government (TFG) and the latter's Ethiopian allies.
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The ARS was formed in 2007 after roughly 400 delegates, including former Islamic Courts Union Shura chairman Sheikh Hassan Dahir Aweys, ICU Executive chairman Sharif Sheikh Ahmad, former TFG Speaker of Parliament Sharif Hassan Sheikh Aden, and the former TFG Deputy Prime Minister Hussein Mohamed Farrah, approved a constitution and central committee.
Islamic extremist organizations that used such a black flag include al‑Qaeda, al‑Shabaab, the Islamic Courts Union, the Islamic State of Iraq and Hizbul Islam (2009).
On August 1, 2006, Farah resigned along with seven other ministers, in protest at Prime Minister Ali Mohammed Ghedi's postponement of talks with the Islamic Courts Union (ICU).
Fighting breaks out between Somali protesters and Ethiopian troops in the town of Beledweyne after an official is arrested for refusing to hand over a member of the ousted Islamic Courts Union.
On 20 December 2006, Salad Ali Jelle, Defence Minister of Somalia's Transitional Federal Government, said that one of Washington's suspects, Abu Taha al-Sudan, was an Islamic Courts Union leader fighting against the Transitional Federal Government in the 2006 Battle of Baidoa.
Fall of Mogadishu (2006): The Transitional Federal Government and Ethiopian Army attacked and captured the city held by the Islamic Courts Union
Somalia's interim government was then resisting advances by the Islamic Courts Union forces north to the last unoccupied city of Baidoa.