East Timor owes its territorial distinctiveness from the rest of Timor, and the Indonesian archipelago as a whole, to being colonised by the Portuguese, rather than the Dutch; an agreement dividing the island between the two powers was signed in 1915. Colonial rule was replaced by the Japanese during World War II, whose occupation spawned a resistance movement that resulted in the deaths of 60,000 people, 13 percent of the population at the time. Following the war, the Dutch East Indies secured its independence as the Republic of Indonesia and the Portuguese, meanwhile, re-established control over East Timor.
Portuguese withdrawal and civil war
According to the pre-1974 Constitution of Portugal, East Timor, known until then as Portuguese Timor, was an "overseas province", just like any of the provinces that made up continental Portugal. "Overseas provinces" also included Angola, Cape Verde, Portuguese Guinea, Mozambique, São Tomé and Príncipe in Africa; Macau in China; and had included the territories of Portuguese India until 1961, when the Prime Minister of India, Jawaharlal Nehru, ordered its invasion and annexation.
In April 1974, the left-wing Movimento das Forças Armadas (Armed Forces Movement, MFA) within the Portuguese military mounted a coup d'état against the right-wing authoritarian Estado Novo government in Lisbon (the so-called "Carnation Revolution"), and announced its intention rapidly to withdraw from Portugal's colonial possessions (including Angola, Mozambique and Guinea, where pro-independence guerrilla movements were fighting since the 1960s).
Unlike the African colonies, East Timor did not experience a war of national liberation. Indigenous political parties rapidly sprang up in Timor: The Timorese Democratic Union (União Democrática Timorense, UDT) was the first political association to be announced after the Carnation Revolution. UDT was originally composed of senior administrative leaders and plantation owners, as well as native tribal leaders. These leaders had conservative origins and showed allegiance to Portugal, but never advocated integration with Indonesia. Meanwhile, Fretilin (the Revolutionary Front of Independent East Timor) was composed of administrators, teachers, and other "newly recruited members of the urban elites." Fretilin quickly became more popular than UDT due to a variety of social programs it introduced to the populace. UDT and Fretilin entered into a coalition by January 1975 with the unified goal of self-determination. This coalition came to represent almost all of the educated sector and the vast majority of the population. The Timorese Popular Democratic Association (Portuguese: Associação Popular Democratica Timorense; APODETI), a third minor party, also sprang up, and its goal was integration with Indonesia. The party had little popular appeal.
By April 1975, internal conflicts split the UDT leadership, with Lopes da Cruz leading a faction that wanted to abandon Fretilin. Lopes da Cruz was concerned that the radical wing of Fretilin would turn East Timor into a communist front. Fretilin called this accusation an Indonesian conspiracy, as the radical wing did not have a power base. On 11 August, Fretilin received a letter from UDT leaders terminating the coalition.
The UDT coup was a "neat operation", in which a show of force on the streets was followed by the takeover of vital infrastructure, such as radio stations, international communications systems, the airport and police stations. During the resulting civil war, leaders on each side "lost control over the behavior of their supporters", and while leaders of both UDT and Fretilin behaved with restraint, the uncontrollable supporters orchestrated various bloody purges and murders. UDT leaders arrested more than 80 Fretilin members, including future leader Xanana Gusmão. UDT members killed a dozen Fretilin members in four locations. The victims included a founding member of Fretilin, and a brother of its vice-president, Nicolau Lobato. Fretilin responded by appealing successfully to the Portuguese-trained East Timorese military units. UDT's violent takeover thus provoked the three-week long civil war, in pitting its 1,500 troops against the 2,000 regular forces now led by Fretilin commanders. When the Portuguese-trained East Timorese military switched allegiance to Fretilin, it came to be known as Falintil.
By the end of August, the UDT remnants were retreating toward the Indonesian border. A UDT group of nine hundred crossed into West Timor on 24 September 1975, followed by more than a thousand others, leaving Fretilin in control of East Timor for the next three months. The death toll in the civil war reportedly included four hundred people in Dili and possibly sixteen hundred in the hills.
Indonesian nationalist and military hardliners, particularly leaders of the intelligence agency Kopkamtib and special operations unit, Opsus, saw the Portuguese coup as an opportunity for East Timor's annexation by Indonesia. The head of Opsus and close Indonesian President Suharto adviser, Major General Ali Murtopo, and his protege Brigadier General Benny Murdani headed military intelligence operations and spearheaded the Indonesia pro-annexation push. Indonesian domestic political factors in the mid-1970s, were not conducive to such expansionist intentions; the 1974–75 financial scandal surrounding petroleum producer Pertamina meant that Indonesia had to be cautious not to alarm critical foreign donors and bankers. Thus, Suharto was originally not in support of East Timor invasion.
Such considerations became overshadowed by Indonesian and Western fears that victory for the left-wing Fretilin would lead to the creation of a communist state on Indonesia's border that could be used as a base for incursions by unfriendly powers into Indonesia, and a potential threat to Western submarines. It was also feared that an independent East Timor within the archipelago could inspire secessionist sentiments within Indonesian provinces. These concerns were successfully used to garner support from Western countries keen to maintain good relations with Indonesia, particularly the United States, which at the time was completing its withdrawal from Indochina. The military intelligence organisations initially sought a non-military annexation strategy, intending to use APODETI as its integration vehicle. Indonesia's ruling "New Order" planned for the invasion of East Timor. There was no free expression in "New Order" Indonesia and thus no need was seen for consulting the East Timorese either.
In early September, as many as two hundred special forces troops launched incursions, which were noted by US intelligence, and in October, conventional military assaults followed. Five journalists, known as the Balibo Five, working for Australian news networks were executed by Indonesian troops in the border town of Balibo on 16 October.