Sabah was not (and supposedly is not) a part of Malaysian territory. As quoted from Wikipedia, the history of integration of Sabah began in 1963 when most ethnic community leaders of Sabah, namely, Tun Mustapha representing the Muslims, Tun Fuad Stephens representing the non-Muslim natives, and Khoo Siak Chew representing the Chinese, would eventually support the formation of Federation of Malaysia.
An agreement was signed by Tunku Abdul Rahman, Harold MacMillan, the British Prime Minister, and William Goode, the last Governor of North Borneo, signed on behalf of the territory on August 1, 1962 putting to paper the agreement to form the union. Indonesia and the Philippines opposed the formation of Mayasia which included Sabah and Sarawak. The Philippines still claimed Sabah as its territory based on the traditional relationship and Sulu Sultanate which was given the claim of Sabah after the Brunei Empire granted Sabah as a Sulunese territory.
Now, an uprising has just begun in the disputed territory of Sabah. Sabah was integrated into Malaysia only under the agreement of adventurers such as Tun Mustapha, Tun Fuad Stephens and Khoo Siak Chew. In 1980's Datuk Pairin Kitingan had questioned legality of Malaysia. Sabah had been under the control Barisan National, except 1985-1994 when Mr. Datuk Pairin Kitingan broke the tradition of Barisan Nasional as powers holder in the whole Malaysia.
With the uprising in Sabah, it is a high time that Indonesian government began to play its roles and influence in meddling the domestic affairs of Malaysia. Indonesia must taka advantage to strengthen its positions along the borders with Malaysia in Sabah and Sarawak.
The Sabah incident was apparently a sign of disintegration of Malaysia. The situation in Sabah was described as tense and the Malaysian government took stern and harsh security measures to face the uprisings. The uprosing was caused both by the claims of the descendents of Sultan Kiram III, the legitimate ruler of Sabah under the Sulu Sultanate and dissatisfaction among the local Sabah residents who were struggling to get more proportional revenues from the rich region.
Indonesia must take steps to take advantage of the uprising in Sabah to strengthen its position as a leading power in the region.
