Independence

Following a UN-sponsored agreement between Indonesia, Portugal and
the United States and a surprise decision by the Indonesian President B. J. Habibie, a UN-supervised popular referendum was held on August 30, 1999,to choose between Special Autonomy within Indonesia and independence. 78.5% of voters chose independence, but violent clashes, instigated primarily by elements within the Indonesian military and aided by Timorese pro-Indonesia militias led by Eurico Guterres, broke out soon afterwards. A peacekeeping force (INTERFET leAustralia)
intervened to restore order. The militias fled across the border into Indonesian West Timor, from which sporadic armed raids were attempted.
As these raids were repelled and international moral opinion forced
Indonesia to withdraw tacit support,[citation needed] the militias dispersed. INTERFET was replaced by a UN force of International Police, the mission became known as UNTAET, and the UNTAET Crime Scene Detachment was formed to investigate alleged atrocities. UNTAET was headed by the late Sérgio Vieira de Mello as UN Transitional Administrator from December 1999 to May 2002. On December 2, 1999,
De Mello established the National Consultative Council (NCC), a
political body consisting of 11 East Timorese and four UNTAET members
charged with overseeing the decision-making process during the
transition period leading to independence. However, UNTAET experienced
difficulties initially in establishing its credibility amongst the
Timorese leadership, leading to street violence. An important workshop on March 1, 2000,
brought the Timorese and UN leadership group together to tease out a
revised strategy, and identify institutional needs. The Timorese
delegation was led by José Ramos-Horta, and included Mari Alkatiri. The outcome was an agreed blueprint for a joint administration with executive powers, including leaders of the National Congress for Timorese Reconstruction (CNRT), led by future president Xanana Gusmão.

Further details were worked out in a conference in May 2000. De Mello
presented the new blueprint to a donor conference in Lisbon,[17] on June 22, 2000, and to the UN Security Council on June 27, 2000.[18] On July 12, 2000, the NCC adopted a regulation establishing a Transitional Cabinet of four East Timorese and four UNTAET representatives.[19] The revamped joint administration successfully laid the institutional foundations for independence, and on September 27, 2002, East Timor joined the United Nations