The war on terror has finally reached Indonesia, but with far-reaching consequences including the potential blurring of the lines between a civilian government and the military, writes Damien Kingsbury from Melbourne The bombing of a nightclub on Saturday, 12 October, in Bali, Indonesia, has resulted in a seismic shift in local and regional politics. The political tensions that have been uncovered by this tragedy have forced the beginning of rapid change in Indonesia and the region. Outsiders had been calling on Indonesia to act on terrorism for more than a year, with no result. However, the bombing, the deaths of almost 200 people and the horrible injuries inflicted on hundreds more have forced Indonesia to take some degree of action. The first major step taken by the government of Indonesia was its recognition that its tolerance of extremism has allowed for the growth of terrorist organisations. Indonesia is home to a large number of Islamist groups who use violence to pursue their goals. These groups include the recently disbanded Laskar Jihad (Holy Warriors), the Laskar Mujahadeen (Warrior Defenders of the Faith), the Front Pembela Islam (FPI -- Islamic Defenders Front), and Jemaah Islamiyah (JI -- Islamic Community). These organisations have been tolerated because they are closely linked to Indonesia's political elite, and often they function as front organisations for elite agendas. The Laskar Jihad was armed and trained by members of the Indonesian military (TNI) to fight against Christians in a communal conflict in Maluku (the Moluccas), where they contributed to the deaths of at least 8,000 people. The Laskar Jihad (LJ) was funded by figures close to former President Suharto, in large part to discredit then President Abdurrahman Wahid. The smaller and even more radical Laskar Mujahadeen has also been fighting in Maluku, mostly around Ambon, and while it has no known links with the military it does receive considerable support from some of the more shadowy organisations in Indonesia. Many members of both organisations had experience fighting in Afghanistan with the Taliban and Al-Qa'eda and there are links between them and organisations like Jemaah Islamiyah. The Front Pembela Islam operates primarily in Java, usually against targets such as nightclubs and other symbols of Western decadence. The FPI is linked to the more fundamentalist elements of Indonesian Islamic parties. However, the group is more a gang of religiously motivated thugs, influenced by elite agendas, than a para- military or terrorist organisation. The JI is the most troubling of all these organisations. Its links with Al-Qa'eda are the most explicit, and its operations the most far-ranging, with members being arrested in the Philippines and Singapore. They conducted a bombing campaign in Manila which led to 22 deaths, and are linked with attempted bombings in Singapore. JI is widely considered to be the South-East Asian branch of Al-Qa'eda. The group is structured in a similar cell-like fashion. Many of its members trained with Al-Qa'eda in the 1990s and it has received funding from Al-Qa'eda sources. Indeed, JI's chief of operations, Riduan Isamuddin, also known as "Hambali", fought with Al-Qa'eda in the 1990s, and is said to have orchestrated a failed-bombing of Western targets in Singapore. The goal of JI is to create an Islamic state across Indonesia, Malaysia, Singapore, southern Thailand and the southern Philippines. The organisation has close links to the Moro Islamic Liberation Front and Abu Saayef organisations in the Philippines. JI leaders also established Malaysia's radical Kampulan Militan Malaysia (KMM), which shares a number of members and is essentially the Malaysian branch of the organisation. Abu Bakar Bashir, the Jemaah Islamiyah leader, is an outspoken admirer of Osama Bin Laden, and an explicit opponent of the West. JI has been identified as the most likely suspect for the 12 October tragedy because it has the motive, the capacity, and the experience. Yet there is support for JI and the Laskar Jihad among Indonesia's Islamic parties and from Indonesia's vice- president, Hamzah Has. Although they only command 37 per cent of the vote based on the 1999 elections, the Islamist vote can be expected to increase in the 2004 elections. It is a vital bloc in determining the next president, and political Islam will draw on sympathy from Muslims in other political organisations. As a result of radical Islam's links to the political and military community, and the "all-or- nothing" nature of religion in politics, the Indonesian government has been reluctant to move against these groups. This has been enhanced by President Megawati Sukarnoputri's general "do nothing" style. This, however, will exacerbate the divide between political Islam and secular parties in Indonesia. More importantly, in this divide, Islamists are likely to line up on one side and secularists will line up on the other along with the military. In such a polarised environment, Islamic extremism is likely to find fertile grounds for further growth. The success by either side will produce a restriction of political freedom. And more dangerously may put the TNI into a more powerful political position. The TNI already determines policy on security and is a powerful force in the cabinet. Australia's greatest achievement following the Bali bombing has been to have its police and intelligence investigators accepted in Indonesia. It is unlikely that these officials will be openly welcomed by their Indonesian counterparts. But in simple terms, Indonesian police investigators are not especially well-trained, have little technical expertise, and are subject to political preferences and pressure. Australia's foreign minister, Alexander Downer, has also held talks with Sukarnoputri about strengthening intelligence links, and support for the TNI's special Kopassus forces. The nature of closer intelligence links is not yet clear, but is likely to revolve around sharing information on terrorism and possibly on Indonesia's separatist movements. However, this closer relationship is unlikely to include sharing information that Australia currently shares primarily with the United States and the United Kingdom. Support for Kopassus is based on that organisation's intelligence and anti-terrorist components. To date, these special forces have been used almost exclusively for internal political purposes, and not aimed at detecting terrorism. Indeed, Kopassus has trained a number of organisations that have employed terrorist methods, including the Laskar Jihad, the East Timor militias, and the militias now operating in Aceh. Moreover, Kopassus has a cloudy background in kidnapping, torture and murder of a wide variety of non-violent political and religious activists. In response to the Bali tragedy, Australia, and inevitably the US, will support a return to an even more military-dominated government. The Indonesian military is keen to renew links with Australia and the US. The TNI is eager to pursue an arms deals with the two nations in order to help in its fight against separatists in Aceh and Papua. But its deep seeded "nationalism" will not allow it to accept any restrictions or any perceived encroachment on Indonesia's narrowly defined sovereignty. The rejection of foreign interference extends to issues such as human rights, with which the TNI has a long and troubled history. Australia and the US have a history of supporting the military for political purposes. This relationship was cultivated during the cold war. Now the war is on "terrorism", and the common belief is that a return to "stability" in Indonesia is more important than the pursuit of reform and democratisation.