There are a variety of stories about Gaddafi's involvement in the region but in general:
A mostly unknown proxy war was fought by Libya under Gaddafi in the 1980s and 1990s against Indonesia and the Philippines.
Gaddafi set up the "World Mathaba Organization" to coordinate and support various separatist insurgencies across the globe, in pro-western countries. Gaddafi supported a number of well known insurgencies like IRA in Northern Ireland and ETA in Spain, and POLISARIO against Morocco.
The Philippines and Indonesia were firmly entrenched in the American side during the Cold War. America supported Philippines against Moros and the Indonesians against West Papuans, East Timorese and Acehnese.
The seperatist organizations which Gaddafi supported in the Philippines were the Moro National Liberation Front, and Moro Islamic Liberation Front, of the various Muslim Moro ethnic groups rebelling against Philippines colonization on Mindanao and Sulu. Gaddafi also establish contacts with Communist insurgents in the Philippines.http://defence.pk/threads/muammar-gaddafis-secret-war-against-indonesia-and-the-philippines-and-france.304268/
The is surely a good summary to begin with.
Does anyone know what he is up to. Did Gaddafi found a kind of Al Qaeda.
Abu Sayyaf is the group most responsible for terrorist attacks on the WTC and they were a splinter cell of the Moro Islamic front.