In Brunei, the Indonesian-backed North Kalimantan National Army revolted on December 8, 1962. They tried to capture the Sultan of Brunei, seize the oil fields and seize European hostages. The Sultan escaped and asked for British help. He received British and Gurkha troops from Singapore. On December 16, British Far Eastern Command claimed that all major rebel centers had been cleared. On April 17 1963, the rebel commander was captured and the rebellion ended.
The Philippines and Indonesia formally agreed to accept the formation of Malaysia after a referendum organized by the United Nations. It was organized in Sabah and Sarawak regions and Malaysia Day was postponed to September 16 so that UN teams could gather votes from Borneo.
After the UN presented a pro-Malaysia report, Indonesian president-for-life Sukarno maintained his anti-Malaysia stand. He claimed that Malaysia would have been only an extension of British colonial rule in the area.
On January 20 1963, Indonesian Foreign Minister Sabandrio announced Indonesia's hostile stand against Malaysia. On April 12, Indonesian volunteers (most likely irregular army troops) begun to infiltrate Sarawak and Sabah for raids, sabotage and propaganda. On July 27 Sukarno declared that he was going to "crush Malaysia". On August 16 troopers of the Gurkha Brigade clashed with 50 Indonesian guerillas.
Despite all this, the Federation of Malaysia was formally formed on September 16, 1963. Only Brunei decided against joining (and Singapore split later).
Two days later 1000 rioters burned down the British embassy in Jakarta. Bomb attacks began with a bomb in Katong Park. Two Indonesian agents were captured. Several hundred rioters sacked the Singapore embassy in Jakarta and the homes of Singapore diplomats. On the other side, crowds attacked the Indonesian embassy in Kuala Lumpur.
The Philippines also broke diplomatic relations with Malaysia.
Indonesian raids from their bases in Kalimantan increased. There were at least 22,000 regular Indonesian troops and 24,000 ethnic Chinese communist sympathizers. They launched their raids in platoon-sized units. The Indonesians apparently thought that Malaysians were ready to rally to their side. They were to be proven mistaken.
In 1964 Indonesian troops begun to raid areas in the Malaysian peninsula. In August 1964, 16 armed Indonesian agents were captured in Johore. Activity of regular Indonesian army attack over the border also increased. The British Royal Navy deployed their forces to defend Malaysia. British Commonwealth forces were formed of 18 British battalions, including elements of Gurkha Brigade and three Malaysian battalions.
British-Malaysian troops were thinly deployed and had to rely on border posts and reconnaissance of commando units. They mainly tried to keep Indonesian troops on their side of the border.
On August 17 Indonesian paratroopers landed on the coast in the south-west of Johore and attempted to establish guerilla groups. On September 2 1964 more paratroopers landed in Labis, Johore. On October 29, 52 soldiers landed in Pontian in Johore-Malacca border and were captured by New Zealand troops.
When the United Nations accepted Malaysia as a nonpermanent member, Sukarno withdrew Indonesia from it and attempted to form Conefo, Conference of New emerging Forces.
In January 1965, Australia agreed to send troops to Borneo after many Malaysian requests. Australian troops included 3 Royal Australian Regiment and Australian Special Air Service.
There were 14,000 British and Commonwealth forces in Borneo at this time. At least officially, British and Australian troops could not follow attackers over the Indonesian border. However, units like the Special Air Service, both the British and Australian versions - did so clandestinely. Australia admitted to these incursions in 1996.
At the end of 1965 Indonesians begun to use Indonesian army regular forces. On June 28, they crossed the border into eastern Sebatik Island near Tawau, Sabah and clashed with defenders.
On September 30, 1965, a Communist coup attempt forced the Indonesian army to concentrate on domestic matters and combat in Malaysia decreased. Rebels killed six senior generals. The Indonesian Army killed thousands of communist supporters in retaliation and General Suharto consolidated his power at Sukarno's expense. In 1966 he forced Sukarno to resign.
In May 28 1966 at a conference in Bangkok, the Malaysian and Indonesian governments declared the conflict over. Violence ended in June. A peace treaty was signed on August 11 and ratified two days later.