With their departure the Afar rose in revolt, burning the Tendaho Plantation and killing many non-Afar in the area around Asayita, as well as closing the highway that linked the Red Sea port of Assab with the rest of the country, bringing a halt to the Ethiopian economy.

Despite this vicious response, Ras Alimirah and his son had been watching developments in Ethiopia, and had prepared accordingly by secretly sending a number of students to Somalia for training in guerrilla warfare.

Afterwards a number of ANLM members were appointed to local administrative positions, which weakened both the ALF's military activity and political influence amongst the Afar.

However the Ethiopian People's Revolutionary Democratic Front (EPRDF) was not happy about its alliance with the ALF due to its conservative ideology, the ALF’s apparently lavish expenditure of the regional budget, its undisguised favor towards the Aussa area for economic development, and the intrigues of the various members of the Alimirah family with regional players.

Despite this announcement, Radio Ethiopia reported on 25 September 2000 that the leader of the ALF, Sultan Alimireh Hanfareh, had returned from exile to meet with Prime Minister Meles Zenawi to discuss political, economic and social issues affecting the Afar region.