The confrontation began in 1963 with Sukarno’s edict of “Crush Malaysia”. It was carried out at a smaller scale, hence the term confrontation, not war, because Indonesia was also wary of dragging the British and the Americans in. It started with incursions into Sabah and Sarawak in North Borneo, before escalating with incursions into Peninsular Malaysia. It was said that the first attack took place at the Tebedu police station in Serian, Sarawak, on 12 April 1963. Corporal John Ramek was the first fallen hero on the Malaysian side in the attack carried out by 10 soldiers from the Indonesian National Army.
The confrontation lost its momentum soon after the failed coup by the Indonesian Communist Party on 1 October 1965 to overthrow the leaders of the Indonesian National Army. The murder of the six generals and an officer enraged the Indonesians. It intensified the secret negotiations between the Malaysians and the Indonesians behind President Sukarno’s back to achieve a truce. After a peace treaty between Malaysia and Indonesia in 1966, Sukarno was forced to step down in 1967. He spent the rest of his life under house arrest until his death in 1970.
Also see in the Wiki: