The use of violence by Muslim militants seeking an independent Islamic State, has a long history in some countries in Southeast Asia, such as Indonesia and the Philippines, which has deep religious and ethnic conflict (Jones, Smith and desmaleza, 2003). After the second world war, the Darul Islam movement unsuccessfully, create an Islamic State in the region of West Java of what became Indonesia (Abuza, 2003). Anti-Government activities associated with this movement continued through the first 1960s.1 reinforced by the Islamic revival in recent decades, some radical Islamic separatist groups emerged at the end of 1980 were more than willing to participate in acts of terrorism, including the Moro Islamic front of liberation (MILF) and the Abu Sayyaf Group (ASG) in the southern Philippines. In the mid-1990s, the AC had formed as a more organized network of people at the margin of the law who were willing to carry out terrorist attacks and other forms of violence to achieve their goals (International Crisis Group, 2002b). The rapid development of the AC as a terrorist group was facilitated by its links with other Islamic separatist groups operating in Southeast Asia, as well as by its direct connections with Al Qaeda. JI and of leaders of the organisation JI emerged from the efforts of two radical Muslim clerics, Abdullah Sungkar and Abu Bakar Ba Ba’asyir, who saw themselves as Muslim descendants of the first separatist movements, such as Darul Islam, and spent decades of work to promote Islamic fundamentalism in Southeast Asia (Abuza, 2003b, p. 126). These Indonesian clerics always with intellectual and ability of organization to the fundamentalist movement Islamic giving rise to joint implementation JJ.2 is seen as one of the many means to achieve an Islamic State that could bring together Islamic true believers residing in different countries of Southeast Asia. AC has also been configured by the jihad people practical experience in Mghanistan and fostered close ties with Al-Qaeda.