[9] This also included the Laskar Jihad militia group, composed of trained fighters from other predominantly Muslim areas of Indonesia, who ran a campaign in the later stages of the conflict to drive out Christian residents of Maluku.

[24] The secession was supported on all sides of the religious and political spectrum as residents shared the same concerns of relative logistical difficulties associated with distances in the region, the expropriation of economic wealth by outside individuals and a distant and disengaged government in Ambon.

[3][24] The redrawing of administrative districts and contention between Tidore and Ternate over the location of the soon-to-be capital cast into doubt the viability of numerous existing power-structures and those employed by the groups that formed these structures.

[3] Economic power in Ambon from the mid-1980s onwards was held by civil servants,[26] observed P. M. Laksono, and their salaries and monetary provisions from Jakarta contributed the overwhelming majority of wealth entering the Maluku region, as local agricultural and marine production was largely subsistence and commercial fishing operations were mostly foreign owned.

[34] The alliances facilitated a relationship to allow peace between villages that were rigidly structured as either wholly Christian or Islamic and had formed the largest political units of Moluccan society prior to the Indonesian state.

[3] In 1999 the Kao and Jailolo claims received backing from the Sultan of Ternate and Protestant ethno-political groups, while the Makianese were supported by Muslim candidates, in their respective attempts to assume governorship of the newly established North Maluku province.

[5] During 1999, the national government agreed with Makian lobbyists to create a new Muslim majority Malifut sub-district, or kecamatan, which incorporated 16 Makianese settlements, several villages of Christian Pagu and Kao and the strategic gold deposits on the disputed lands.

[40] Soon-to-be president Abdurrahman Wahid indicated that the individual personally responsible for the Ambon unrest was Yorrys Raweyai, the leader of mercenary group Pancasila Youth that had been known to act as hired "muscle" for the Suharto administration activities.

[21][52][54] It is widely recorded that the initial confrontation that sparked the conflict was between a Bugis minibus driver and either some Christian youths,[3][31][55] a drunk[56] or a Muslim conductor,[31] near a bus terminal in Batu Merah village.

Despite the differing accounts, it is agreed that a mob, Church reports state some 600 people,[31] of Muslim residents gathered and marched upon the Christian areas of Batu Merah at approximately 16:00 (UTC+9), where they torched numerous houses and several businesses by Mardika market.

[31] The group had been driven on by incorrect rumors that the local mosque had been torched and faced little opposition from the police force, which only fielded ten lightly armed intelligence members due to the holiday.

[31] On the night of 19 January, witnesses report that large, and allegedly well organised, groups of Christian rioters entered Kampung Paradeys in several waves, smashing and looting from Muslim homes on the orders of an unknown leader.

[31] At least one Butonese school-girl was among several reported killed during the rioting at Gunung Nona, struck by a machete and placed in a sack,[31] and other bodies were found during the following days in the ashes of destroyed buildings, trapped by the rapidly moving flames.

[31][60] Despite the efforts by residents of both faiths to prevent an assault, the following day Hila village proper was allegedly attacked by a Wakal mob, who murdered one person and looted and torched numerous, mostly Christian, houses.

[53] In the first recorded confrontation of security forces and the rioting public several, reportedly Christian, rioters were shot and at least one killed following the stabbing murder of a Balinese member of the Kostrad Strategic Reserve Command in the coastal neighbourhoods of Benteng,[31][52] though the order of events is disputed.

[31] The fighting became more virulent with the reported murder of 5 Butonese passengers of a van near the state Islamic institute by a Christian mob, and a further 8 people were killed in Karang Panjang and Kramat Jaya as homes and a mosque were set alight.

[31] The largest loss of life at the hands of security forces at that stage in the conflict occurred in Kariu on the island of Haruku, when military units used live ammunition to quell a clash between a groups of Christian residents and Muslims from surrounding villages, reportedly killing 23.

[42][59][74][75] Accounts differ as to how many died on either side and the total number of dead from the shooting and confrontation may have been around 30, including 4 elderly residents who attempted to flee to the forest to escape the complete destruction of Kariu and the town's main church by the Muslim mob.

[58][76] Another altercation between youths concerning an 'insult to Islam' on 27 March[77] is alleged to have started wide scale violence on the Kei Islands, south east of Ambon, that claimed up to 80 lives during the first weeks of April, with particularly fierce fighting happening in the capital Tual.

[58][86] The dispute happened days after a peace deal was agreed upon by local leaders of the two faiths,[86] and it was therefore clear that the resentment and violence could not be contained by the formalities of an authority distrusted on both sides after the role of security forces in so many deaths.

[15] On 27 July, three members of a rioting Muslim crowd were killed by police directly outside the Al-Fatah mosque,[92] however few instances of intervention with live fire by security forces were recorded with concrete details.

[93] The residents were allegedly locked in the Yabok church and fired on by people wearing uniforms of an elite special forces unit, killing around 25 unarmed civilians, including a priest and children, and the bodies were later burned by a Muslim mob.

[98] In the period between the first riots in Ambon and September 1999, humanitarian organisation Kontras estimated 1,349 had died in communal fighting[15] and that tens of thousands had been displaced to ad hoc refugee centres or other provinces.

[102] The intense fighting heralded the widespread use of firearms and home-made bombs by civilian gangs, and claimed at least 68 lives and caused the destruction of the symbolic Silo Church in Ambon City on 26 December.

[104] Up to 42 people were killed on neighbouring Seram Island over three days during a raid by Muslim militias on the predominantly Christian town of Alang Asaudi on 3 December, and government forces were criticized for not preventing such a high number of casualties.

[108] On 4 January 2000, at least 17 were killed by live ammunition as police opened fire on clashing mobs in Masohi, a port town on Ceram Island, where several hundred houses were also destroyed by arson.

[3][117][118] In hindsight the document was an act of blatant provocation likely forged by Makianese bureaucrats, however on 3 November the Reverend Riskotta was viciously murdered by a Muslim mob in Tidore while attending a meeting to discuss concerns with the officials, having been escorted there by police.

[3][120] The Sultan's guard had both established secure perimeters around areas of the city, including the mostly Chinese-owned business district, and physically stood between the mobs and possible victims in some cases and were later commended for preventing a potential massacre.

[3][121] The targeting of churches for destruction and rumors that a number of children were killed by the Makianese fighters, along with descriptions of the security forces' inability to protect local Christians in Tidore and Ternate, prompted Halmahera residents to construct homemade weapons to defend themselves.

[126] Older minors perpetrated armed assaults against rival forces or civilian targets, while both elementary and secondary school children helped construct the homemade weapons that were predominant in the first year of the conflict.