Indonesia: Timor-Leste (East Timor)

Dormant, with continued violence. Muslim Indonesian occupation of Catholic Timor, with complex consequences.
 
East Timor is 97% Roman Catholic (from Portuguese colonial times), blended with the traditional animist beliefs of the Timorese. On de-colonialisation, Timor declared independence in 1975, then to be invaded by Indonesia, US-backed, for allegedly anti-communist reasons.
 
There were 60-200,000 deaths during the initial occupation, and 100,000 further deaths up to 1999, followed by Indonesian Muslim settlement.
 
UN-supported independence came in 1999, after much violence and many atrocities, with destruction of villages and widespread social deterioration. Catholic alignment increased during Muslim Indonesian occupation. Civic revival has been slow, still with outbreaks of violence. Currently, Timor-Leste risks returning to violence, as a result of poor living conditions and post-occupation complexities such as corruption and communal violence.
 

Links:

Wikipedia: Religion in East Timor
Library of Congress: Irian Jaya and East Timor