Indonesia annexed East Timor the following year, and under President Suharto, its occupation of the territory was often characterised by violence and brutality.

Up until 1999, Indonesia was faced with constant pressure and criticism from the United Nations and the international community regarding its occupation of East Timor.

[2] More pressure on Indonesia followed when two East Timorese leaders - Bishop Carlos Ximenes Belo and José Ramos-Horta - received the Nobel Peace Prize in 1996.

Habibie succeeded Suharto in March 1998, and sought reform on the East Timor issue with international pressure mounting.

East Timor youths from July to September 1998 conducted a free speech campaign that demonstrated to the "UN and the Indonesian government their rejection of autonomy and endorsement of an UN-supervised referendum.

In the preceding months, President Habibie had made various public statements whereby he mentioned that the costs of maintaining monetary subsidies to support the province were not balanced by any measurable benefit to Indonesia.

[6] The agreement between the Indonesian and Portuguese governments included a "Constitutional Framework for a special autonomy for East Timor" as an annexe.

[10] Special four wheel drive vehicles were flown into East Timor by the United Nations in order to cope with local conditions.

[10] The Indonesian government did not invest much time or resources in demonstrating to the people of East Timor the benefits of retaining its autonomy with the state.

[13] Voters were presented with the two following options:[14] The aftermath of the referendum results saw mass violence, killings and destruction targeted at the East Timorese.

It concluded that the post referendum violence "took the form of vengeance" and included "executions, gender violence ("women were targeted for sexual assault in a cruel and systematic way"), destruction of 60 to 80 percent of both public and private property, disruption of up to 70 percent of the health services, and the displacement and forcible relocation of thousands of people to West Timor".

[13] [verification needed] When the UN returned to East Timor from 22 October after being forced to leave for genuine fear for its members, they found the territory destroyed with a population largely missing or terrified.

"[6] Most of the trained professionals in East Timor happened to be Indonesian or Indonesia sympathisers, who largely left the territory after the results of the referendum.