In the meantime Singapore's "full independence" depended on her joining Malaya. If this happened it would have changed the population structure of Malaya and the Chinese would have become the majority race. To avoid this Tungku Abdul Rahman the Prime Minister of Malaya proposed the formation of Malaysia which would include Singapore, Sabah, Sarawak and Brunei. This was agreeable to the British but Sukarno felt that if Malaysia became a reality, his dream of a Greater Indonesia would be destroyed. So he opposed the formation of Malaysia and on12th April 1963 a small party of Indonesians conducted a raid across the border into Sarawak.
In Brunei a rebel organization called the North Kalimantan National Army (TNKU) had somewhat a similar idea of establishing a confederation of the Borneo states of Brunei, Sabah and Sarawak with the Sultan of Brunei as the head of state. Though poorly organized and equipped it set out on 8th December 1962 to "kidnap" the Sultan and capture the vital installations. The Sultan avoided capture and troops airlifted from Malaya were able to put down the greater part of the rebellion within a few days. On 17 April 1963 the rebel leader was captured and the rebellion came to an end.
Apart from Singapore none of the other states had been part of Malaya. Since Britain was going to give away Sabah, Philippines saw an opportunity to extend its territory and made claim on Sabah. None of the States involved wanted a major conflict between them. Through diplomatic negotiations Sukarno, Tunku and President Macapagal of Philippines met in Manila on June 1963 and formed an association called MAPHILINDO and agreed on the formation of Malaysia if the United Nation confirmed that the people of Sabah and Sarawak wanted to be part of Malaysia.
When the UN confirmed that the people of Sabah and Sarawak were in favor of merging with Malaya, Tunku's proposal of "Malaysia" became a reality but without Brunei on 16th September 1963. But Sukarno failed to keep his word Instead he broke off diplomatic relations and declared that he would crush Malaysia. If Sukarno had hoped for a similar scenario as that of Indonesia obtaining independence form the Dutch with minor military action, then he was mistaken. Britain was determined to ensure that Malaysia remained a reality and Brunei survived as an independent state. Malaysian and Commonwealth forces were deployed to deal with the Indonesian forces border incursions.
Indonesia's domestic political and economic situation was not conducive to any major military action though attempts were made to land seaborne and airborne troops in peninsular Malaysia. The Indonesian Communist Party was competing with the Indonesian Army for political power. Indonesia isolated itself by withdrawing from the UN when Malaysia was made a member of the Security Council and worsened its economic situation. Thus the "Confrontation" only provided Sukarno with a mean to hold the people together and retain his presidency. But unfortunately his presidency came to an abrupt end when a communist coup was launched.
On 30th September 1965 a group of communist calling themselves G30S proclaimed a new revolutionary regime after having murdered six of the top ranking army generals and discarding their corps in a well at the Halim Air Force Base. But the coup was short lived because Major General Suharto, the commander of the Strategic Division based in Bandong swiftly retaliated and seized the initiative and eased Sukarno out of his presidency. As the political power shifted to the Indonesian Army and the Indonesian Communist Party's influence declined the "Confrontation" was terminated on 11th August 1966.
Post "Confrontation" era saw good relationship and cooperation between the Indonestion and Malaysian Armies. I accompanied General Tungku Osman Jewa the Chief of Armed Forces Staff on the first military delegation that went to Indonesia. We were taken to Suharto's simple ordinary house and there was no ambiguity in the discussion that followed. This set the pace for the rapid development of bilateral joint military exercises. From opponents we became the best of friends.