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Now parliament has dismissed the country's first democratically-elected president Abdurrahman Wahid for corruption and misrule.
Mr Wahid has repeatedly warned that his removal would mean the end for Indonesia, with regions including Aceh and the Moluccas breaking away.
New President Megawati Sukarnoputri is committed to national unity and is expected to resist pressure from separatist movements.
There have been outbreaks of sustained religious and ethnic violence in different parts of the sprawling archipelago, as well as renewed calls from some areas for independence.
These aspirations were fuelled in 1999 by the end of Indonesian rule in East Timor, though the violent chaos which accompanied it also serves as a warning to others.
Ensuring real stability is one of the biggest challenges facing Indonesia's leaders.
Click on the places named on the map to learn more about Indonesia's flashpoints