In June 1980, Goukouni, representing the People's Armed Forces (Forces Armées Populaires--FAP) faction in Chad and nominally the president of the Interim Government of National Unity (GUNT), signed a military cooperation treaty with Libya. In October he requested direct military assistance from Qaddafi. In the course of 1980, Libya sent up to 15,000 troops into Chad and by December Libyan forces had firm control of the Chadian capital and most other urban centers outside the south. Habré, representing the Northern Armed Forces (Forces Armées du Nord-- FAN) faction in Chad, fled to Sudan, vowing to resume the struggle.
Although Libyan intervention enabled Goukouni to win militarily, the association with Qaddafi created diplomatic problems. In January 1981, when Goukouni and Qaddafi issued a joint communiqué stating that Chad and Libya had agreed to "work for the realization of complete unity between the two countries," an international uproar ensued. Although both leaders later denied any intention to merge their states politically, the diplomatic damage had been done.
Throughout 1981 most of the members of the OAU, along with France and the United States, encouraged Libyan troops to withdraw from Chad. One week after the "unity communiqué," the Organization of African Unity's committee on Chad met in Togo to assess the situation. In a surprisingly blunt resolution, the twelve states on the committee denounced the union goal as a violation of the 1979 Lagos Accord, called for Libya to withdraw its troops, and promised to provide a peacekeeping unit, the Inter-African Force (IAF). Goukouni was skeptical of OAU promises, but in September he received a French pledge of support for his government and the IAF.
But as Goukouni's relations with the OAU and France improved, his ties with Libya deteriorated. One reason for this deterioration was that the economic assistance that Libya had promised never materialized. Another, and perhaps more significant, factor was that Qaddafi was strongly suspected of helping Goukouni's rival, Acyl Ahmat, leader of the Democratic Revolutionary Council (Conseil Démocratique Révolutionnaire--CDR). Both Habré and Goukouni feared Acyl because he and many of the members of the CDR were Arabs of the Awlad Sulayman tribe. About 150 years earlier, this group had migrated from Libya to Chad and thus represented the historical and cultural basis of Libyan claims in Chad.
As a consequence of the Libya-Chad rift, Goukouni asked the Libyan forces in late October 1981 to leave, and by mid-November 1981 they had withdrawn to the disputed Aouzou Strip.