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Separatism has plagued Indonesia since its independence. This dissertation examines four cases of separatism in Indonesia, including the South Moluccas, West Papua, and East Timor, as well as one case where separatism did not emerge, Sumba. It describes sovereignty in Indonesia since its inception, considering ideological challenges including communist, Islamist, and federalist, and concludes that sovereignty in Indonesia was tenuous prior to the New Order period (1965-1998). Using case study methodology, each case is examined to determine the predominant factors that led to separatism, including the role of elites, poverty, the method of incorporation, religion and culture, and political participation. It then examines Sumba in the context of these variables to determine why a separatist movement did not emerge in that region, despite a juridical basis for separatism. Political participation, social continuity, and the role of the elites prove to be the deciding factors in the emergence of separatism. This dissertation also examines the factors that led to the defeat of separatists in the South Moluccas, the persistence in West Papua, and the success in East Timor and concludes that the causes of the emergence of separatism are not the same as the causes of the persistence of separatism. This dissertation makes four significant contributions to the field. The first is through a detailed case-study approach comparing three regions that have undergone serious separatist movements in the state of Indonesia as well as a 'negative case.' The second contribution is the differentiation between the causes of the emergence of separatism and the causes of the persistence of separatism. The third contribution this dissertation makes is toward a better understanding of the relationship between nationalism and separatism. Finally, when taken together, these three elements combine to challenge predominant theories of separatist conflict that emphasize one causal factor over others, including, for example, poverty, ethnicity or religion. It also raises doubts about the applicability of theories of anti-state violence in states that are beginning the consolidation process, or as they incorporate territory after the consolidation process has been long under way, as in the cases of West Papua and East Timor.
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