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Washington has accused the Union of Islamic Courts, which threatened to overrun the government, of trying to turn the country into a safe haven for terrorists and demanded the handover of three suspects who it believes were behind the bombing of its embassies in east Africa.
Islamist leaders abandoned their city to the clans late on Wednesday night. Many of their militiamen simply melted away in the face of Ethiopian tanks and warplanes.
Ali Mohamed Gedi, whose government has so far had little support in the capital, has been locked in negotiations with tribal leaders about how to take control.
A source close to the government said that the prime minister had asked the elders to take over administration of the city in return for information about three men suspected of masterminding attacks on American embassies in Nairobi and Dar es Salaam.
“The message they forwarded was that there are certain people wanted by the international community and by us and if you can tell us their whereabouts we would appreciate it, and that would be a sign of collaboration,” he said.
The request was made in a private meeting with leaders of the Habar Gidir clan. Their Ayr sub-clan is believed to be sheltering Fazul Abdullah Mohamed, from the Comoros Islands, Saleh Ali Saleh Nabhan, a Kenyan, and Abu Taha al-Sudan, from Sudan.
The men were named in June by Jendayi Frazer, the US assistant secretary of state for African affairs, as the three most wanted terrorist suspects America was seeking in connection with simultaneous car bombs at the US embassies in Nairobi and Tanzania, which killed 257 people in 1998.
Washington believes the same cell was behind an attack four years later on a hotel near the Kenyan coastal resort of Mombasa, which left 13 people dead, and an unsuccessful attempt to shoot down an Israeli airliner.
After the attack, the men slipped away through Kenya’s island archipelago to Somalia’s lawless capital. With no immigration department, police force or central government since 1991, they could readily disappear into Mogadishu’s warren of bullet-riddled buildings. The anarchic capital, one of the most dangerous places on earth, was off-limits to foreign security agents.
Six months ago it was seized by Islamic militias loyal to Sheikh Hassan Dahir Aweys, himself listed by America as a terrorist. Aweys fled with the rest of the Islamic leadership on Wednesday night. Somalian government troops, backed by Ethiopian soldiers, arrived in the outskirts of Mogadishu hours later.
The city has been rocked ever since by the sound of gunshots as looters ransacked properties used by the courts and clan militias. Ethiopian tanks took up strategic positions at the airport and the long abandoned American embassy.
While some residents welcomed the arrival of government forces, others said they feared a return to the anarchy they knew before the courts and militias arrived.
“Things are very tense,” said Sahal Hayir, a student. “We have heard about people being shot and that the warlords’ militias are back and we are hoping that the government can make the city safe like the courts did.”
Matt Bryden, a Somalia analyst in Nairobi, warned that the defeat of the courts could leave a power vacuum if the government and the Ethiopians failed to find a quick political solution.
“There are arms everywhere in Mogadishu. It is a tinderbox. The government has to tread very carefully,” he said.
Meanwhile, Somali soldiers have begun reopening police stations established by the courts as the first step towards a sweep of the battle-scarred city for terrorists and foreign jihadis.
As well as Al-Qaeda suspects, Ethiopia is keen to root out its own rebel opposition who have used Somalia as a base from which to launch attacks along its eastern border region.
Ethiopia’s army is the second largest in Africa and the most feared on the continent. Apache helicopters and Russian-built warplanes began airstrikes last Sunday and some 6,000 troops are now estimated to be in Somalia. The country is a key ally in the American-led war on terror and US troops have been training Ethiopian troops and advising on border security.
With Ethiopia backing the interim government, its sworn enemy Eritrea has been sending arms and fighters to bolster the Islamic courts, raising fears of a regional conflict.
A United Nations arms monitoring report published earlier this year detailed how members of Ethiopia’s rebel Ogaden National Liberation Front and its Oromo Liberation Front, also engaged in a guerrilla war against the government, were supplied with arms from Eritrea via Somalia.
Hundreds of fighters also travelled from the eastern region of Ethiopia to Aweys’s tribal homeland for training.
Bereket Simon, special adviser to the Ethiopian prime minister, said: “All terrorist and extremist groups that are a threat to the region must be brought under control and these people are at the top of the list.”
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