Final answer:
Torture was used in Indonesia to suppress separatist movements and assert control over East Timor during a bitter civil war that followed the annexation of East Timor.
Step-by-step explanation:
Torture in Indonesia regarding East Timor was a result of a bitter civil war that led to the annexation of East Timor by Indonesia in 1976. Control over East Timor was only relinquished in 1999 following years of conflict and separatist movements. The use of torture during this period can be understood as part of the violent tactics used to suppress independence movements and maintain control over annexed territories, a practice not uncommon in the history of colonial and military occupations.