The Maluku Islands are home to a diverse population, with their role as the centre of the Dutch spice trade in the colonial period leaving a distinct legacy and a sizeable Christian community. In the central islands such as Ambon, this Christian community constituted half of the population.1 In the tense climate following the fall of Suharto and the violence in Poso, a minor dispute involving a bus driver sparked three days of riots in the city of Ambon in January 1999. Violence between migrants and indigenes, and Muslims and Christians, spread into the surrounding area. At least 48 people were killed and swathes of Ambon, including churches and mosques, were destroyed.2 In February, the conflict spread to the rest of Ambon island, with much of the fighting involving attacks on villages and towns that were home to minority populations or violent clashes over control of mixed conurbations. The efforts of regional and national authorities to maintain stability floundered, with many local security personnel becoming embroiled in the conflict and poor infrastructure preventing the deployment of reinforcements. Fighting continued throughout 1999, devastating Ambon city and inspiring Laskar Jihad (a militant Islamic organisation with ties to some hard-line elements within the Indonesian security forces) to enter the fray in early 2000.3 The introduction of modern weapons and trained militants changed the dynamic of the conflict, putting predominantly Christian “Red” forces on the backfoot and driving thousands of civilians from their homes.4
In June 2000, the Government of Indonesia declared a state of emergency and employed a new strategy to contain the conflict. A battalion of elite troops (Yon Gab) was formed and deployed to Maluku in place of units which had sided with one community or the other. While much of the intercommunal violence ended shortly after the state of emergency was declared, these troops gave government security forces the edge they needed to prevent intercommunal violence and stop Laskar Jihad from perpetuating the conflict.5 This operation served to halt the fighting until the broader security situation in Indonesia improved. In February 2002, negotiations between Christian and Muslim community leaders from Maluku mediated by an Indonesian government minister culminated with the signing of an 11-point declaration in the town of Malino. Known as the Malino II Peace Accord, this agreement ended the conflict and created the framework for peace to return to the area.6 Laskar Jihad laid down their arms after the October 2002 Bali Bombings.