Separatists holding out in East Timor against Indonesian rule have two counterparts in the outer reaches of the world's largest archipelago.
One trouble spot is the Special Region of Aceh, conservatively Muslim and historically rebellious, at the tip of Sumatra. In the 17th Century, Aceh had a cavalry with Persian horses, an elephant corps and a navy strong enough to hold off the Portuguese.
The other is 3,100 miles to the east: the former Dutch territory of West Irian, which has been the Indonesian province of Irian Jaya since 1963 and shares the island of New Guinea with independent Papua New Guinea.
The colonial Dutch never really succeeded in bringing Aceh under control and fought a war with the local sultan that lasted 35 years, until 1903.
When the Japanese occupied Sumatra in 1942, Aceh declared itself independent. When the Dutch tried to recolonize after World War II, Aceh resisted.
Aceh was cool to the idea of joining newly independent Indonesia, and declared itself an independent Islamic republic in 1951. That happened after the Indonesians made the mistake of trying to incorporate it into the province of North Sumatra.
Only when it was designated in 1967 as a Special Region did Aceh agree to end its rebellion in exchange for a promises that it would have a measure of real autonomy.
Autonomy did not materialize, but Banda Aceh, the provincial capital, has its own laws on culture, religion and education. In a country that portrays itself as a secular humanist state with a belief in one god but freedom of worship, Aceh is the most fervently Muslim region.
A new independence movement emerged in the mid-1970s when the Aceh Merdeka (Free Aceh) movement began supporting armed guerrillas. It was believed to have been smothered years ago, but some officials say it has revived in recent months.
Ambush killings that started in April are blamed variously on drug gangs, army deserters and Libyan-trained rebels. At least 26 people were reported slain in a three-week period.
The killers are officially known as members of a "security disturbing movement," or GPK from the Indonesian words gerakan pengacau keamanan. This generic label is applied to all separatist groups, in an apparent attempt to detract from the seriousness of rebel threats.
In Irian Jaya, the Organisasi Papua Merdeka (Free Papua Movement) has been fighting for either independence or a merger with Papua New Guinea ever since incorporation into Indonesia became final.
The Dutch had promised the Irianese they would have independence someday, but then-President Sukarno pushed Indonesia's claim to West Irian.
Indonesian troops invaded in 1962 and the United States helped prod Indonesia and the Netherlands into negotiations under auspices of the United Nations.
Jakarta was awarded administrative control of West Irian in 1963, with the understanding that a free election would determine the former colony's status. In 1969, tribal chiefs voted unanimously to incorporate it into Indonesia.
This "act of free choice" was criticized at the time for not being a vote of the people.