Although considerable wealthy, the Sultan of Brunei had a court that was corrupt and ridden with intrigues. Consequently, the sultan found difficulty in extending control to many of his datus throughout the domain, rebellion and strife was frequent in the sultanate. It was under this circumstances that the territory, comprising most of what is now Sabah State, was ceded to the neighboring sultanate as the prize for military assistance.
The murder of the 12th Sultan of Brunei, Muhammad Ali, by Bendehara Abdul Mubin resulted to civil war. The perpetrator claimed the throne but was contested by Pengeran Bongso, a nephew and son-in-law of the deceased sultan. Both contestants to the throne asked the support of Badarud-din, a relative of both and the reigning Sultan of Sulu. Badarud-din was unable to solve the crisis, but supported Pengeran Bongso (who took the name Sultan Muaddin). Sultan Muaddin emerged victorious and the large territorial land known today as “the State of Sabah” was ceded to the Sultanate of Sulu in exchange of the military help and support.
The observation of the contemporary British officer will give us more insight of the territory ceded:
“The first material alteration in the sovereignty of the territorial possession took place in the kingdom of Borneo Proper, when his Raja was obliged to call in the aid of the Solos to defend him against an insurrection of the Maruts and Chinese. In consideration of this important aid, the Raja of Borneo Proper ceded to the Sultan of Solo all that portion of Borneo then belonging to him, from Kimanis in latitude 5° 30’ north to Tapean-durian, in the straits of Macassar, which include the whole north of Borneo.”
The sultanate’s connection with Northern Borneo goes back as early as 1521, as far as the written record is concerned, when a Brunei Sultan was married to a Sulu princess. This early connection between the two sultanates cemented the familial relationship. This political marriage developed into a politico-military allegiance.
Meanwhile, as trade flourished in the region, the mercantilist policies adapted by the colonial powers deprived the Sultanate of Bornei and Sulu of their own profitable commercial activity. Thus driven into piracy and smuggling, the Sulus and the Bruneis continually menaced western trade, presenting a problem that was to persist for many years.