In March 1967, Sukarno was stripped of his remaining power by Indonesia's provisional Parliament, and Suharto was named Acting President. His most significant pillar of support, the PKI, was effectively eliminated by the other two pillars-the army and political Islam and the army was on the way to unchallenged power. Sukarno's balancing act of 'Nasakom' (nationalism, religion and communism) had unravelled. It is possible that over one million people were imprisoned at one time or another. Although killings occurred across Indonesia, the worst were in the PKI strongholds of Central Java, East Java, Bali, and northern Sumatra. Thousands of local vigilantes and army units killed actual and alleged PKI members.

They started in the capital, Jakarta, and spread to Central and East Java and, later, Bali. The massacres began in October 1965, in the weeks following the coup attempt, and reached their peak over the remainder of the year before subsiding in the early months of 1966. Communists were purged from political, social, and military life, and the PKI itself was banned. The failed coup released pent-up communal hatreds which were fanned by the Indonesian Army, which quickly blamed the PKI. The upheavals led to the downfall of President Sukarno and the commencement of Suharto's three-decade dictatorship.

The purge was a pivotal event in the transition to the 'New Order' and the elimination of the Indonesian Communist Party (PKI) as a political force.

The most widely accepted estimates are that between 500,000 to more than one million people were killed, with some estimates as high as two to three million. Initially it began as an anti-communist purge following a controversial coup by the army (30 September Movement) in Indonesia. The Indonesian killings of 1965–1966 (sometimes referred to as the Indonesian Massacres, Indonesian Genocide, or Indonesian Politicide ) were large-scale killings which occurred in Indonesia over many months, targeting communists, ethnic Chinese and alleged leftists, often at the instigation of the armed forces and government.

The jakarta method