ARPCT was a secular group believed to be funded by the United States CIA, due to concerns their primary rivals for control of the city, the Islamic Courts Union (ICU), was alleged to have links to al-Qaeda and to be harboring al-Qaeda members. The International Crisis Group, which had direct contacts with the warlords, said in June 2006 that the CIA was funnelling $100,000 to $150,000 a month to the ARPCT.
Events in Mogadishu were mostly peaceful in the first phase of the fighting starting February 18 until May 7 when fighting erupted and the alliance lost battle after battle. Somali Sheikh Hassan Dahir Aweys said on Radio Shabelle, the violence was started by the people who have proclaimed themselves to be fighters against terrorism. ICU forces defeated the ARPCT and gained control of Mogadishu by June 5.
Dubbed the Second Battle of Mogadishu, the defeat forced ARPCT forces to surrender or flee. Some remained in Somalia while others, such as warlords Mohamed Dheere and Mohamed Afrah Qanyare, went to Ethiopia seeking refuge.
Both warlords since returned to fight against the ICU in the ensuing war, and are resuming their places in Mogadishu following the Fall of Mogadishu to the Transitional Federal Government and Ethiopian forces in December 2006.