Indonesia experienced a sharp rise in international and domestic terrorism during the year, as weakening central government control and a difficult transition to democracy provided fertile ground for terrorist activities. Several bombings occurred in 2000, two of which targeted official foreign interests. Unidentified assailants detonated a car bomb in front of the Philippine Ambassador's residence in central Jakarta as the Ambassador was entering the compound on 1 August. The explosion killed two Indonesians, seriously injured three other persons – including the Ambassador – and slightly injured 18 bystanders, including one Filipino and two Bulgarians. Unidentified perpetrators also conducted a grenade attack against the Malaysian Embassy on 27 August, but no injuries resulted.
Six other bombings from July to November targeted domestic interests in the capital. The most destructive occurred on 13 September when a car bomb in the Jakarta stock exchange's underground parking garage killed 10 Indonesians. Other targets included the Attorney General's office, the Jakarta Governor's residence, a Jakarta hotel, a local nongovernmental organization, as well as the Ministry of Agriculture, which was used as the courtroom venue for former President Soeharto's corruption trial. Multiple bombings also occurred in major cities in North Sumatra, Riau, and East Java.
Indonesian officials made little progress in apprehending and prosecuting those responsible for the bombings. The Indonesian National Police arrested 34 persons suspected of involvement in the Malaysian Embassy and the stock-exchange bombings, but a lack of evidence forced the release of all suspects in mid-October. The police claim the Free Aceh Movement (GAM) – a group seeking an independent state in northern Sumatra – conducted both attacks and planned another against the US Embassy to "create chaos" in Jakarta. The evidence made public as of December, however, does not support elements of this theory. Nevertheless, the GAM or Achenese separatists did conduct sporadic attacks on ExxonMobil oil facilities in Aceh early in the year. The group's primary target was Indonesian security elements, some of which continued to guard ExxonMobil facilities.
Indonesian nationalists and some radical Islamist groups occasionally carried out violent protests outside US diplomatic facilities in response to perceived US interference in domestic affairs and support for Israel. One demonstration culminated in a mob attack against the US Consulate in Surabaya on 15 September, and another involved the Islamist militant Front Pembela Islam (Islamic Defenders' Front) threatening US citizens in the country. Other Islamist extremists in October searched for US citizens in a central Javanese city, warning them to leave the country.
Militiamen attacked a UNHCR aid office in Atambua, West Timor, on 6 September, killing three aid workers, including one US citizen. Suspected militia members also killed two UN peacekeepers – a New Zealander and a Nepalese national – during the year.