The island of Timor was first colonized by Portugal in 1520 and had been controlled by them for about three centuries. The Dutch had been in control of many of the surrounding islands and eventually invaded Timor. In 1860 a treaty was made that divided the island into east and west (western being controlled by the Netherlands and East being controlled by Portugal). Eventually the Netherlands gave up their colonies giving rise to now Indonesia. Portugal then gave up East Timor and the Timorese Democratic Union was independent for nine days before being invaded and annexed by Indonesia. In 1976 East Timor was officially declared the 27th province of Indonesia.
It is said that more than 200,000 people died due to famine, disease, and fighting after annexation. In 1983 the UN called for independence and self determination for East Timor but this only worsens conditions and even more fighting takes place between rebels and Indonesia. At the time Portugal was stills recognized as the administrative power of East Timor by the UN and grants political asylum to all people of East Timor. Then, in 1997 the Australian-East Timor Association reported human rights violations against woman by Indonesian armed forces. Due to the Asian Economic Crisis of 1997 former President Suharto resigned and new President B.J. Habibie took office. Habibie agreed to hold a referendum on East Timor independence which sparked anti-independence groups of Timor to act in violence and intimidation campaigns including the killing of 57 civilians in a churchyard. After 25 years of Indonesian rule, East Timor civilians voted to secede causing pro-Jakarta and Indonesian armies to kill hundreds of civilians and force around 500,000 to leave their homes.
In 1999 the UN forces Indonesia to leave East Timor. East Timor was then governed by the UN for the next three years. East Timor then declared independence on May 20, 2002. Overall, reports of 200,000 of the original 650,000 Timorese people were killed in this conflict.
The people of East Timor were unsatisfied with the governing of Indonesia and blamed much of the famine on them. Indonesia invaded East Timor because they saw an opportunity to easily accumulate a large amount of land due to the chaos of the area and under-developed government. Plus, if East Timor declared independence, this could set the precedent for the other provinces of Indonesia to gain independence.
My suggestion for peace would call for all the complete independence of East Timor and to allow the UN to send in peacekeepers to temporarily make sure Indonesia does not try to take any of their land. The only way to ensure peace is for the two countries to respect the borders of their states and build a relationship through trade.