[7] The intervention of Laskar Jihad soon gave Muslims the upper hand in the conflict,[8] with the Islamists burning down churches and houses of the indigenous Melanesian communities in Ambon and other Moluccan islands.

[13] In February 2002, the Malino II Accord between Muslims and Christians was signed, which demanded among other things the withdrawal of Laskar Jihad from the Maluku Islands.

[7] After the Bali bombings in October 2002, Laskar Jihad announced its alleged disbandment, but soon made a new appearance when it established an office in Sorong in the province of West Papua.

In May 2003, reports smuggled out of Papua claimed arson and machetes had been used to destroy ten townships, their food gardens and livestock, sending the surviving women and children into jungle hiding from their pursuers.

Although at first a newly created military unit, the Joint Battalion, took action against Laskar Jihad in Maluku, it was replaced in mid-2001 by Kopassus, which was more sympathetic towards the militia.

"[5] Laskar Jihad leader Jafar Umar Thalib has voiced public support for the establishment of an Islamic theocracy in Indonesia.

[25] However, scholars have noted that fatwas issued by Salafi muftis from the Arab Peninsula played a significant role in the formation of Laskar Jihad.

[26] It has also been argued that Thalib's efforts to distance himself from al-Qaeda and anything related to it were made in the context of the September 11 terror attacks when the Indonesian government exerted strong pressure on Laskar Jihad not to exploit anti-American sentiment.