Editing Sabah (section)

== History ==
{{main|History of Sabah}}

===Prehistory===
{{main|Prehistoric Malaysia}}
[[File:Madai Sabah Madai-Cave-01.jpg|thumb|Entrance to the [[Madai Cave]]]]
The earliest known human settlement in the region existed 20,000–30,000 years ago, as evidenced by stone tools and food remains found by excavations along the [[Darvel Bay]] area at Madai-Baturong caves near the Tingkayu River.<ref name= "MacKinnon1996">{{cite book |author=Kathy MacKinnon |title=The Ecology of Kalimantan |url= https://books.google.com/books?id=70iB6Tf62OkC&pg=PA55 |year= 1996 |publisher=Periplus Editions |isbn= 978-0-945971-73-3 |pages= 55–57 |quote=Since 1980, the Sabah Museum staff have carried out excavations in the Madai and Baturong limestone massifs, at caves and open sites dated back 30,000 years. Baturong is surrounded by large area of alluvial deposits, formed by the damming of the Tingkayu River by a lava flow. The Tingkayu stone industry shows a unique level of skills for its period. The remains of many mammals, snakes, and tortoises were found, all food items collected by early occupants of the rock shelters.}}</ref> The earliest inhabitants in the area were thought to be similar to [[Aboriginal Australians]], but the reason for their disappearance is unknown.<ref name="sabah info">{{cite web |url=http://www.sabah.edu.my/kaupin/guest/sabah/sabah_forever.htm |title=About Sabah |work=Sabah Tourism Promotion Corporation and Sabah State Museum |publisher=Sabah Education Department |access-date=15 May 2016 |archive-url=https://web.archive.org/web/20160515105207/http://www.sabah.edu.my/kaupin/guest/sabah/sabah_forever.htm |archive-date=15 May 2016 }}</ref> In 2003, archaeologists discovered the Mansuli valley in the [[Lahad Datu District]], which dates back 235,000 years.<ref>{{cite web |url=http://www.thestar.com.my/news/nation/2012/04/10/archaeologists-hit-gold-at-mansuli/ |title=Archaeologists hit 'gold' at Mansuli |author=Durie Rainer Fong |work=The Star |date=10 April 2012 |access-date=26 April 2016 |archive-url=https://web.archive.org/web/20141030100432/http://www.thestar.com.my/News/Nation/2012/04/10/Archaeologists-hit-gold-at-Mansuli/ |archive-date=30 October 2014 }}</ref> The archaeological site at [[Skull Hill, Malaysia|Skull Hill]] (''Bukit Tengkorak'') in [[Semporna District]] was the largest pottery making site in [[Neolithic]] Southeast Asia.<ref>{{cite web |url= http://www.seaa-web.org/bulletin2008/bul-essay-08-01.htm |title=Prehistoric Sites and Research in Semporna, Sabah, Malaysia |author=Stephen Chia |publisher= Centre for Archaeological Research Malaysia, University of Science, Malaysia | work=Bulletin of the Society for East Asian Archaeology |year=2008 |access-date=23 May 2016 |archive-url=https://web.archive.org/web/20160523083324/http://www.seaa-web.org/bulletin2008/bul-essay-08-01.htm |archive-date=23 May 2016 }}</ref><ref>{{cite web |url=http://www.museum.sabah.gov.my/?q=content/bukit-tengkorak-archaeological-sites-semporna |title= Bukit Tengkorak Archaeological Sites, Semporna |publisher=Sabah Museum Department |access-date=26 April 2016 |archive-url=https://web.archive.org/web/20160325001742/http://museum.sabah.gov.my/?q=content%2Fbukit-tengkorak-archaeological-sites-semporna |archive-date=25 March 2016 }}</ref>

=== Sultanates of Brunei and Sulu influences ===
During the 7th century AD, a settled community known as Vijayapura, a tributary to the [[Srivijaya]] empire, was thought to have existed in northwest Borneo.<ref name="Hutton2000">{{cite book |author=Wendy Hutton |title=Adventure Guides: East Malaysia |url=https://books.google.com/books?id=YWO5Va53GkgC&pg=PA31 |access-date=26 May 2013 |date= 2000 |publisher=Tuttle Publishing |isbn=978-962-593-180-7 |pages=31–57}}</ref><ref name= "Bala2005">{{cite book| author=Bilcher Bala|title=Thalassocracy: a history of the medieval Sultanate of Brunei Darussalam|url=https://books.google.com/books?id=-bQuAQAAIAAJ&q=vijayapura+p%27o-ni| year=2005| publisher=School of Social Sciences, University Malaysia Sabah|isbn=978-983-2643-74-6|page=30}}</ref> The earliest independent kingdom in Borneo, supposed to have existed from the 9th century, was Po Ni, as recorded in the Chinese geographical treatise ''[[Taiping Huanyu Ji]]''. It was believed that Po Ni existed at the mouth of [[Brunei River]] and was the predecessor to the Bruneian Empire.<ref name="Bala2005"/><ref>{{cite book |author1=Barbara Watson Andaya |author2=Leonard Y. Andaya |title=A History of Malaysia |url= https://books.google.com/books?id=5GSBCcNn1fsC&pg=PA57 |access-date=26 May 2013 |year=1984 |publisher=Palgrave Macmillan |isbn=978-0-312-38121-9 |page= 57}}</ref> When China was conquered by the [[Mongol Empire]], all Chinese vassal states were subsequently controlled by the Mongol emperors of China. Early in 1292, [[Kublai Khan]] is said to have sent an expedition to northern Borneo,<ref name= "Runciman2011">{{cite book |author= Steven Runciman |title=The White Rajah: A History of Sarawak from 1841 to 1946 |url= https://books.google.com/books?id=m4_O9GB4KBoC&pg=PA14 |date= 2011 |publisher=Cambridge University Press |isbn=978-0-521-12899-5 |page=14}}</ref> before departing for the [[Mongol invasion of Java|invasion of Java]] in 1293.<ref>{{cite web |url= https://www.ccel.org/g/gibbon/decline/volume2/chap64.htm |title=Fall In The East — The Decline And Fall Of The Roman Empire [Chapter 64] |author= Edward Gibbon |publisher=[[Christian Classics Ethereal Library]] |year=1788 |access-date=18 October 2017 |quote=Hundred thousand Chinese imitated his example; and the whole empire, from [[Mongol invasions of Vietnam|Tonkin]] to the [[Great Wall of China|great wall]], submitted to the dominion of [[Kublai Khan|Cublai]]. His boundless ambition aspired to the conquest of [[Mongol invasions of Japan|Japan]]: his fleet was twice shipwrecked; and the lives of a hundred thousand Mongols and Chinese were sacrificed in the fruitless expedition. But the neighbouring kingdoms, Corea, [[Tonkin]], [[Cochinchina]], [[Pegu]], [[Bengal]], and [[Tibet]], were reduced in different degrees of tribute and obedience by the effort or terror of his arms. He explored the Indian Ocean with a fleet of a thousand ships: they sailed in sixty-eight days, most probably to Borneo, under the equinoctial line; and though they returned not without spoil or glory, the emperor was dissatisfied that the savage king had escaped from their hands.}}</ref><ref>{{cite book |author= Henry Miers Elliot |title=The History of India, as Told by Its Own Historians: The Muhammadan Period |url= https://books.google.com/books?id=-knEHQUmBFgC&pg=PA27 |year= 2013 |publisher=Cambridge University Press |isbn=978-1-108-05585-7 |page=27}}</ref> As a result of this campaign, it is believed that many of his followers in addition to other Chinese traders eventually settled and established their own enclave at [[Kinabatangan River]].<ref name="Runciman2011"/>

In the 14th century, Brunei and Sulu were part of the Majapahit Empire but in 1369, Sulu and the other Philippine kingdoms successfully rebelled and Sulu even attacked Brunei which was still a Majapahit [[tributary state|tributary]],<ref>{{cite book|author=Brunei|title=Brunei Darussalam|url=https://books.google.com/books?id=QYa6AAAAIAAJ&q=brunei+majapahit+province|year=2004|publisher=Broadcasting and Information Department, Prime Minister's Office}}</ref> the Sulus specifically invaded Northeast Borneo at Sabah<ref>Ming shi, 325, p. 8411, p. 8422.</ref> the Sulus were then repelled but Brunei became weakened.<ref>{{cite book|author1-link=John N. Miksic|author1=John Norman Miksic|author2=Goh Geok Yian|title=Ancient Southeast Asia| url=https://books.google.com/books?id=zjklDwAAQBAJ&pg=PA501|date=2016|publisher=Taylor & Francis|isbn=978-1-317-27904-4|page=501}}</ref> In 1370, Brunei transferred its allegiance to [[Ming dynasty]] China.<ref name="Chinese records">{{cite web |url=http://nccur.lib.nccu.edu.tw/bitstream/140.119/68001/1/015101.pdf |title=Malaysia-Philippines Territorial Dispute: The Sabah Case |author1=Mohammad Al-Mahdi Tan Kho |author2=Hurng-yu Chen |publisher=NCCU Institutional Repository |work=[[National Chengchi University]] |date=July 2014 |access-date=9 May 2016 |archive-url=https://web.archive.org/web/20160509133532/http://nccur.lib.nccu.edu.tw/bitstream/140.119/68001/1/015101.pdf |archive-date=9 May 2016 }}</ref><ref name="Vienne2015">{{cite book|author=Marie-Sybille de Vienne|title=Brunei: From the Age of Commerce to the 21st Century|url=https://books.google.com/books?id=IfpIBwAAQBAJ&pg=PA42|year= 2015|publisher=NUS Press|isbn=978-9971-69-818-8|page=42}}</ref> The [[Maharaja]] Karna of Borneo then paid a visit to [[Nanjing]] with his family until his death.<ref>{{cite book |author=Shih-shan Henry Tsai |title=The Eunuchs in the Ming Dynasty |url=https://books.google.com/books?id=Ka6jNJcX_ygC&pg=PA152 |year=1996 |publisher=SUNY Press |isbn=978-0-7914-2687-6 |page=152}}</ref> He was succeeded by his son Hsia-wang who agreed to send tribute to China once every three years.<ref name="Chinese records"/><ref name="Vienne2015"/> After that, Chinese [[Junk (ship)|junks]] came to northern Borneo with cargoes of spices, [[bird nest]]s, shark fins, [[camphor]], [[rattan]] and [[pearl]]s.<ref name="Wise1846">{{cite book |author=Henry Wise |title=A Selection from Papers Relating to Borneo and the Proceedings at Sarāwak of James Brooke ... |url=https://books.google.com/books?id=CpBeAAAAcAAJ&pg=PR10 |year=1846 |publisher=publisher not identified |page=10}}</ref> More Chinese traders eventually settled in Kinabatangan, as stated in both Brunei and Sulu records.<ref name="Chinese records"/><ref name="sabah edu">{{cite web |url=http://www.sabah.edu.my/itma135/history.htm |title=History of Sabah |publisher=Sabah Education Department |access-date=14 May 2016 |archive-url=https://web.archive.org/web/20160514040125/http://www.sabah.edu.my/itma135/history.htm |archive-date=14 May 2016 }}</ref> A younger sister of [[Ong Sum Ping]] (Huang Senping), the governor of the Chinese settlement then married [[Sultan Ahmad of Brunei]].<ref name="Chinese records"/><ref>{{cite web |url=http://www.pusat-sejarah.gov.bn/sultanbrunei.htm |title=Sultan-Sultan Brunei |trans-title=Sultans of Brunei |language=ms |publisher=Government of Brunei |access-date=27 January 2017 |archive-url=https://web.archive.org/web/20170128124306/http://www.pusat-sejarah.gov.bn/sultanbrunei.htm |archive-date=28 January 2017 }}</ref> Perhaps due to this relationship, a burial place with 2,000 wooden coffins, some estimated to be 1,000 years old, were discovered in [[Agop Batu Tulug Caves]] and around the Kinabatangan Valley area.<ref name="coffins">{{cite web |url=http://www.thestar.com.my/news/community/2007/04/10/coffins-dating-back-1000-years-are-found-in-the-kinabatangan-valley/ |title=Coffins dating back 1,000 years are found in the Kinabatangan Valley |author=Haslin Gaffor |work=[[Bernama]] |publisher=The Star |date=10 April 2007 |access-date=22 October 2017 |archive-url= https://web.archive.org/web/20171022141115/http://www.thestar.com.my/news/community/2007/04/10/coffins-dating-back-1000-years-are-found-in-the-kinabatangan-valley/ |archive-date=22 October 2017 }}</ref><ref>{{cite web |url= http://www.newsabahtimes.com.my/nstweb/fullstory/9939 |title=Intriguing resting place |author=Rozella Mahjhrin |publisher= | work= [[New Sabah Times]] |date=30 September 2016 |access-date=22 October 2017 |archive-url=https://web.archive.org/web/20171022140719/http://www.newsabahtimes.com.my/nstweb/fullstory/9939 |archive-date=22 October 2017 }}</ref> It is believed that this type of funeral culture was brought by traders from [[Mainland China]] and [[Indochina]] to northern Borneo as similar wooden coffins were also discovered in these countries.<ref name="coffins"/> This was in addition to the discovery of [[Chinese ceramics]] from a shipwreck in [[Tanjung Simpang Mengayau]] estimated to be from between 960 and 1127 AD from the Song dynasty and the Vietnamese [[Đông Sơn drum]] in Bukit Timbang Dayang on [[Banggi Island]] that was between 2,000 and 2,500 years old.<ref name="sabah info"/><ref>{{cite news |url= http://dailyexpress.com.my/news.cfm?NewsID=101912 |title=More shipwrecks lurk off Sabah |newspaper=Daily Express |date=29 July 2015 |access-date=8 February 2017 |archive-url= https://web.archive.org/web/20170208132511/http://dailyexpress.com.my/news.cfm?NewsID=101912 |archive-date=8 February 2017 }}</ref><ref name="Ooi2015">{{cite book |author=Ooi |first=Keat Gin |author-link=Keat Gin Ooi |url=https://books.google.com/books?id=LcM0CwAAQBAJ&pg=PA22 |title=Brunei: History, Islam, Society and Contemporary Issues |publisher=Routledge |year=2015 |isbn=978-1-317-65998-3 |pages=22–110 |via=Google Books}}</ref>

During the reign of Sultan [[Bolkiah]] of Brunei between 1485 and 1524, the sultanate extended over northern Borneo and the [[Sulu Archipelago]], as far as ''[[Maynila (historical entity)|Kota Seludong]]'' (present-day [[Manila]]) with its [[sphere of influence|influence]] extending as far of [[Banjarmasin]],<ref>{{cite book |author=Graham Saunders |title=A history of Brunei |url=https://books.google.com/books?id=SQ4t_OJgSjAC&pg=PA40 |access-date=26 May 2013 |year=2002 |publisher=Routledge |isbn=978-0-7007-1698-2 |page=40| via= Google Books}}</ref> taking advantage of maritime trade after the [[Capture of Malacca (1511)|fall of Malacca to the Portuguese]].<ref name= "HoltLambton1977">{{cite book |author1=P. M. Holt |author2=Ann K. S. Lambton |author3=Bernard Lewis |title=The Cambridge History of Islam: Volume 2A, The Indian Sub-Continent, South-East Asia, Africa and the Muslim West |url= https://books.google.com/books?id=y99jTbxNbSAC&pg=PA129 |date= 1977 |publisher=[[Cambridge University Press]] |isbn=978-0-521-29137-8 |page=129| via= Google Books}}</ref><ref>{{cite book |author1=Barbara Watson Andaya |author2=Leonard Y. Andaya |title=A History of Early Modern Southeast Asia, 1400–1830 |url= https://books.google.com/books?id=0Rh2BgAAQBAJ&pg=PA159 |date= 2015 |publisher= Cambridge University Press |isbn=978-0-521-88992-6 |page=159| via= Google Books}}</ref> Many [[Bruneian Malay people|Brunei Malays]] migrated to Sabah during this period, beginning after the Bruneian conquest of the territory in the 15th century.<ref name= "Brunei migration">{{cite news |url= http://www.bt.com.bn/golden-legacy/2011/10/24/search-brunei-malays-outside-brunei |title=In search of Brunei Malays outside Brunei |author= Rozan Yunos |newspaper=The Brunei Times |date=24 October 2011 |access-date=28 December 2012 |archive-url=https://web.archive.org/web/20160514083428/http://www.bt.com.bn/golden-legacy/2011/10/24/search-brunei-malays-outside-brunei |archive-date=14 May 2016 }}</ref> But plagued by internal strife, civil war, piracy and the [[Western imperialism in Asia|arrival of western powers]], the Bruneian Empire began to shrink. The first Europeans to visit Brunei were the Portuguese, who described the capital of Brunei at the time as surrounded by a [[stone wall]].<ref name="HoltLambton1977"/> The Spanish followed, arriving soon after [[Ferdinand Magellan]]'s death in 1521, when the remaining members of his expedition sailed to the islands of Balambangan and Banggi in the northern tip Borneo; later, in the [[Castilian War]] of 1578, the Spanish who had sailed from [[New Spain]] and had taken Manila from Brunei, unsuccessfully declared war on Brunei by briefly occupying the capital before abandoning it.<ref name="Group"/><ref name="Ooi2015"/><ref name= "Sidhu2009">{{cite book |author= Jatswan S. Sidhu |title=Historical Dictionary of Brunei Darussalam |url=https://books.google.com/books?id=Bry0sOwstIMC&pg=PR53 |date= 2009 |publisher=Scarecrow Press |isbn=978-0-8108-7078-9 |page=53| via= Google Books}}</ref> The Sulu region gained its independence in 1578, forming the [[Sultanate of Sulu]].<ref>{{cite book |first1=Trudy |last1=Ring |first2=Robert M. |last2= Salkin |first3=Sharon |last3=La Boda |title=International Dictionary of Historic Places: Asia and Oceania |url= https://books.google.com/books?id=vWLRxJEU49EC&pg=PA160 |date= 1996 |publisher=Taylor & Francis |isbn=978-1-884964-04-6 |page=160| via= Google Books}}</ref>

When the [[Brunei Civil War|civil war broke out in Brunei]] between sultans [[Abdul Hakkul Mubin]] and [[Muhyiddin of Brunei|Muhyiddin]], the Sultan of Sulu asserted their claim to Brunei's territories in northern Borneo.<ref name="Sidhu2009"/><ref name="myph">{{cite web |url= http://www.ums.edu.my/fksw/images/files/IsuPemilikanWilayahPantaiTimurSabahSatuPenelusurandaripadaSudutSumberSejarah.pdf |title=Isu Pemilikan Wilayah Pantai Timur Sabah: Satu Penulusuran daripada Sumber Sejarah |trans-title=Issues of Ownership of Sabah's East Coast Region: A Study from Historical Sources |author=Eko Prayitno Joko |language=ms, en |publisher=[[Universiti Malaysia Sabah]] |access-date=19 May 2016 |archive-url=https://web.archive.org/web/20160519044519/http://www.ums.edu.my/fksw/images/files/IsuPemilikanWilayahPantaiTimurSabahSatuPenelusurandaripadaSudutSumberSejarah.pdf |archive-date=19 May 2016 }}</ref> The Sulus claimed that Sultan Muhyiddin had promised to cede the northern and eastern portion of Borneo to them in compensation for their help in settling the civil war.<ref name= "Sidhu2009"/><ref name="Brunei history">{{cite book |author=Bachamiya Abdul Hussainmiya |title=Brunei: revival of 1906: a popular history |url= https://books.google.com/books?id=Q7UuAQAAIAAJ |year=2006 |publisher=Brunei Press |isbn=978-99917-32-15-2| via= Google Books}}</ref> The territory seems have not been ceded formally, but the Sulus continued to claim the territory, with Brunei weakened and unable to resist.<ref name="ssc">{{cite news |url= http://www.bt.com.bn/2013/03/07/sabah-and-sulu-claims |title=Sabah and the Sulu claims |author=Rozan Yunos |newspaper=The Brunei Times |date=7 March 2013 |access-date=20 September 2013 |archive-url=https://web.archive.org/web/20140617035533/http://www.bt.com.bn/2013/03/07/sabah-and-sulu-claims |archive-date=17 June 2014 }}</ref> After the war with the Spanish, the area in northern Borneo began to fall under the influence of the Sulu Sultanate.<ref name="Sidhu2009"/><ref name="Brunei history"/> The [[Seafarers|seafaring]] [[Bajau people|Bajau]]-[[Tausūg people|Suluk]] and [[Illanun people]] then arrived from the Sulu Archipelago and started settling on the coasts of north and eastern Borneo,<ref>{{cite book |author=James Francis Warren |title= Iranun and Balangingi: globalization, maritime raiding and the birth of ethnicity |url= https://books.google.com/books?id=w1_3-ff6u-gC&pg=PA409 |date= 2002 |publisher=NUS Press |isbn=978-9971-69-242-1 |page=409| via= Google Books}}</ref> many of them fleeing from the oppression of [[Spanish East Indies|Spanish colonialism]].<ref name="Indonesian demographic">{{cite book |title=Mencari Indonesia: demografi-politik pasca-Soeharto |trans-title=Finding Indonesia: post-Soeharto demographic politics |url=https://books.google.com/books?id=oLVTKSefAtIC&pg=PA123 |year=2007 |language=id | via= Google Books |publisher=Yayasan Obor Indonesia |isbn=978-979-799-083-1 |page=123}}</ref> While the thalassocratic Brunei and Sulu sultanates controlled the western and eastern coasts of Sabah respectively, the interior region remained largely independent from either kingdoms.<ref>{{cite book |author=Ranjit Singh |title=The Making of Sabah, 1865–1941: The Dynamics of Indigenous Society |url=https://books.google.com/books?id=j9xuAAAAMAAJ |year=2000 |publisher=University of Malaya Press |isbn=978-983-100-095-3| via= Google Books}}</ref> The [[Sultanate of Bulungan]]'s influence was limited to the Tawau area,<ref>{{cite book |author=R. Haller-Trost |title=The Contested Maritime and Territorial Boundaries of Malaysia: An International Law Perspective |url=https://books.google.com/books?id=65VuAAAAMAAJ |date= 1998 |publisher=Kluwer Law International |isbn=978-90-411-9652-1| via= Google Books}}</ref> which came under the influence of the Sulu Sultanate before gaining its own rule after the 1878 treaty between the British and Spanish governments.<ref>{{cite book |author=Burhan Djabier Magenda |title=East Kalimantan: The Decline of a Commercial Aristocracy |url=https://books.google.com/books?id=f9T74ges6DIC&pg=PT42 |year=2010 |publisher=Equinox Publishing |isbn=978-602-8397-21-6 |page=42| via= Google Books}}</ref>

=== British North Borneo ===
{{main|North Borneo Chartered Company|North Borneo|Madrid Protocol of 1885}}
{{multiple image
| align             = right
| image1            = Concession of Sabah (Brunei) 1877.jpg
| width1            = 160
| caption1          = The first concession treaty was signed by Sultan [[Abdul Momin]] of Brunei on 29 December 1877<ref name="century"/>
| image2            = Concession of Sabah (Sulu) 1878.jpg
| width2            = 160
| caption2          = The second concession treaty was signed by Sultan [[Jamal ul-Azam]] of Sulu on 22 January 1878<ref name="ssc"/>
| caption_align     = center
| header            = Concession of Sabah
}}
In 1761, [[Alexander Dalrymple]], an officer of the British [[East India Company]], concluded an agreement with the Sultan of Sulu to allow him to set up a trading post in northern Borneo, although this was to prove a failure.<ref>{{cite book |author= Howard T. Fry |title=Alexander Dalrymple (1737–1808) and the Expansion of British Trade |url= https://books.google.com/books?id=flfYsDjH_M4C&pg=PA72 |access-date=25 May 2013 |year=1970 |publisher=Routledge |isbn=978-0-7146-2594-2 |page=68–| via= Google Books}}</ref> Following the [[British occupation of Manila]] in 1763, the British freed Sultan [[Azim ud-Din I of Sulu|Alimuddin]] of Sulu from the Spanish and allowed him to return to his throne;<ref name="Sulu Archipelago">{{cite web |url= https://archive.org/stream/ahz9503.0001.001.umich.edu#page/29/mode/1up/search/British |title=The Sulu Archipelago and its people |author= Sixto Y. Orosa |publisher=Yonkers on Hudson, N. Y., World Book Company, [[University of Michigan]]| via= Internet Archive |year=1931 |access-date=26 August 2016 |page=29}}</ref> this was welcomed by the Sulu people and by 1765, Dalrymple managed to obtain [[Balambangan Island]] off the north coast of Borneo, having concluded a Treaty of Alliance and Commerce with the Sultan Alimuddin as a sign of gratitude for the British aid.<ref name="Brunei history"/><ref name="Sulu Archipelago"/> A small British factory was then established in 1773 on the island.<ref name= "Brunei history"/> The British saw the island as a suitable location to control the trade route in the East, capable of diverting trade from the Spanish port of [[Manila]] and the Dutch port of [[Batavia, Dutch East Indies|Batavia]] especially with its strategic location between the [[South China Sea]] and [[Sulu Sea]].<ref name="Brunei history"/> But the British abandoned the island two years later when [[Piracy in the Sulu Sea|Sulu pirates]] began attacking.<ref name="sabah edu"/> This forced the British to seek refuge in Brunei in 1774, and to temporarily abandon their attempts to find alternative sites for the factory.<ref name="Brunei history"/> Although an attempt was made in 1803 to turn Balambangan into a military station,<ref name="sabah edu"/> the British did not re-establish any further trading posts in the region until [[Stamford Raffles]] [[Founding years of modern Singapore|founded Singapore]] in 1819.<ref name="Brunei history"/>

In 1846, the Sultan of Brunei ceded the island of [[Labuan]] on the west coast of Sabah to Britain through the [[Treaty of Labuan]], and in 1848 it became a [[Crown Colony of Labuan|British Crown Colony]].<ref name="sabah edu"/> Seeing the presence of British in Labuan, the American consul in Brunei, Claude Lee Moses, obtained a ten-year lease in 1865 for a piece of land in northern Borneo. Moses then passed the land to the [[American Trading Company of Borneo]], owned by [[Joseph William Torrey]], [[Thomas Bradley Harris]] and Chinese investors.<ref name="sabah edu"/><ref name="Fitzgerald2016">{{cite book |author=Robert Fitzgerald |title=The Rise of the Global Company: Multinationals and the Making of the Modern World |url= https://books.google.com/books?id=rTkACwAAQBAJ&pg=PA75 |date= 2016 |publisher=Cambridge University Press |isbn=978-0-521-84974-6 |page=75| via= Google Books}}</ref> The company choose [[Kimanis]] (which they renamed "Ellena") as a site for a settlement. Requests for financial backing from the US government proved futile and the settlement was later abandoned. Before he left, Torrey managed to sell all his rights to the Austrian Consul in Hong Kong, [[Gustav Overbeck|Gustav von Overbeck]]. Overbeck then went to Brunei, where he met the [[Temenggong]] to renew the [[Concession (territory)|concession]].<ref name="Fitzgerald2016"/> Brunei agreed to cede all territory in northern Borneo under its control, with the Sultan receiving an annual payment of 12,000 [[Spanish dollar]]s, while the Temenggong received a sum of 3,000.<ref name="Brunei history"/>

In 1872, the Sultanate of Sulu granted use of an area of land in the Sandakan Bay to William Frederick Schuck, a former agent of the German consular service who had lived on the Sulu island of [[Jolo]] since 1864. The arrival of German warship {{SMS|Nymphe|1863|6}} at the Sulu Sea in 1872 to investigate the [[Spanish–Moro conflict|Sulu-Spanish conflict]] made the sultanate believe Schuck was connected with the [[Government of Germany|German government]].<ref>{{cite book |author= Leigh R. Wright |title=The Origins of British Borneo |url= https://books.google.com/books?id=9SzxAQAAQBAJ&pg=PA134 |date= 1988 |publisher=Hong Kong University Press |isbn=978-962-209-213-6 |page=134| via= Google Books}}</ref> The sultanate authorised Schuck to establish a trading port to monopolise the [[rattan]] trade in the northeast coast, where Schuck could operate freely, without the Spanish blockade.<ref>{{cite book |author= James Francis Warren |title=The Sulu Zone, 1768–1898: The Dynamics of External Trade, Slavery, and Ethnicity in the Transformation of a Southeast Asian Maritime State |url= https://books.google.com/books?id=_UyVI5IxcjIC&pg=PA114 |year=1981 |publisher=NUS Press |isbn=978-9971-69-004-5 |pages=114–122| via= Google Books}}</ref> He continued this operation until this land also was ceded to Overbeck, with the Sultan receiving an annual payment of $5,000, by a treaty signed in 1878.<ref name="Brunei history"/>

After a series of transfers, Overbeck tried to sell the territory to [[German Empire|Germany]], [[Austria-Hungary]] and [[Kingdom of Italy|Italy]] but they rejected his offer.<ref name="Fitzgerald2016"/> Overbeck then co-operated with the British Dent brothers ([[Alfred Dent]] and Edward Dent) for financial backing to develop the land, with the Dent company persuading him that any investors would need guarantees of British military and diplomatic support.<ref name="Fitzgerald2016"/> Overbeck agreed to this co-operation, especially with regard to the counterclaims of the Sultan of Sulu, part of whose territory in the Sulu Archipelago had been occupied by Spain.<ref name="Fitzgerald2016"/> Overbeck, however, withdrew in 1879 and his treaty rights were transferred to Alfred Dent, who in 1881 formed the North Borneo Provisional Association Ltd to administer the territory.<ref>{{cite book |author=Charles Alfred Fisher |title= South-East Asia: A Social, Economic and Political Geography |url= https://books.google.com/books?id=dHsOAAAAQAAJ&pg=PA147 |access-date=26 May 2013 |year=1966 |publisher=Taylor & Francis |page= 147 |id=GGKEY:NTL3Y9S0ACC| via= Google Books}}</ref><ref>{{cite book |author=J. M. Gullick |title=Malaysia and Its Neighbours |url= https://books.google.com/books?id=ykM9AAAAIAAJ&pg=PA148 |year= 1967 |publisher=Routledge & K. Paul |isbn=978-0-7100-4141-8 |pages= 148–149| via= Google Books}}</ref><ref>{{cite book |author=Keat Gin Ooi |title=Southeast Asia: A Historical Encyclopedia, from Angkor Wat to Timor. R–Z. volume three |url= https://books.google.com/books?id=QKgraWbb7yoC&pg=PA251 |access-date=26 May 2013 |year=2004 |publisher=ABC-CLIO |isbn=978-1-57607-770-2 |page=251| via= Google Books}}</ref> In the following year, [[Kudat]] was made its capital but due to frequent pirate attacks, the capital was moved to [[Sandakan]] in 1884.<ref name="Hutton2000"/> To prevent further disputes over intervention, the governments of the United Kingdom, Spain and Germany signed the [[Madrid Protocol of 1885]], recognising the sovereignty of the [[King of Spain]] over the Sulu Archipelago in return for the relinquishment of all Spanish claims over northern Borneo.<ref>{{cite web |url=http://www.lawnet.sabah.gov.my/Lawnet/SabahLaws/Treaties/Protocol%28Madrid%29.pdf |title=British North Borneo Treaties. (British North Borneo, 1885) |author=British Government | work= lawnet.sabah.gov.my |publisher= Sabah State Government (State Attorney-General's Chambers) |year= 1885 |access-date=24 February 2013 |archive-url=https://web.archive.org/web/20131029195606/http://www.lawnet.sabah.gov.my/Lawnet/SabahLaws/Treaties/Protocol%28Madrid%29.pdf |archive-date=29 October 2013 }}</ref> The arrival of the company brought prosperity to the residents of northern Borneo, with the company allowing indigenous communities to continue their traditional lifestyles, but imposing laws against [[headhunting]], [[ethnic conflict|ethnic feuds]], [[History of slavery|slave trade]], and piracy.<ref name="Skutsch2013">{{cite book |author=Carl Skutsch |title=Encyclopedia of the World's Minorities |url=https://books.google.com/books?id=yXYKAgAAQBAJ&pg=PA679 |date= 2013 |publisher= Routledge |isbn=978-1-135-19388-1 |page=679| via= Google Books}}</ref><ref name="bnbm">{{cite web |url=http://web.usm.my/km/KM%20XIX,2-2001/THE%20LEGEND%20BY%20SUE%20HARRIS.pdf |title=The Legend by Sue Harris: A Critique of the Rundum Rebellion and a Counter Argument of the Rebellion |author=Callistus Fernandez |work=Department of Sociology, National University of Singapore |language=ms, en |publisher=[[Universiti Sains Malaysia]] |year=2001 |access-date=2 June 2016 |archive-url=https://web.archive.org/web/20160602154850/http://web.usm.my/km/KM%20XIX,2-2001/THE%20LEGEND%20BY%20SUE%20HARRIS.pdf |archive-date=2 June 2016 }}</ref> North Borneo then became a [[protectorate]] of the United Kingdom in 1888 despite facing local resistance from 1894 to 1900 by [[Mat Salleh Rebellion|Mat Salleh]] and [[Antanum]] in 1915.<ref name="sabah edu"/><ref name="bnbm"/>

=== Second World War ===
{{main|Battle of Borneo (1941–1942)|Japanese occupation of British Borneo|Battle of North Borneo}}
[[File:Japanese civilians and soldiers, Tawao (AWM 121707).JPG|thumb|[[Japanese prisoners of war in World War II|Japanese civilians and soldiers]] prior to their embarkation to Jesselton after their surrender to the [[Second Australian Imperial Force|Australian Imperial Force]] (AIF) in [[Tawau]] on 21 October 1945.]]
The Japanese forces landed in Labuan on 3 January 1942,<ref>{{cite book| author=Gordon L. Rottman|title=World War II Pacific Island Guide: A Geo-military Study|url=https://books.google.com/books?id=ChyilRml0hcC&pg=PA206|year=2002|publisher=Greenwood Publishing Group|isbn=978-0-313-31395-0|page=206}}</ref> during the [[Second World War]], and later invaded the rest of northern Borneo.<ref name="sabah edu"/> From 1942 to 1945, Japanese forces occupied North Borneo, along with most of the rest of the island, as part of the [[Empire of Japan]]. The British saw Japanese advances in the area as motivated by political and territorial ambitions rather than economic factors.<ref>{{cite book |author=Takashi Shiraishi |title=The Japanese in Colonial Southeast Asia |url=https://books.google.com/books?id=6mfCzrbOn80C&pg=PA54 |date= 1993 |publisher=SEAP Publications |isbn=978-0-87727-402-5 |page=54| via= Google Books}}</ref> The residing British and the locals were compelled to obey and gave in to the brutality of the Japanese.<ref name="Three Came Home">{{cite AV media |people=[[Claudette Colbert]], [[Patric Knowles]] |url=https://youtube.com/watch?v=W5dNa0O18wQ  |archive-url=https://ghostarchive.org/varchive/youtube/20211211/W5dNa0O18wQ| archive-date=11 December 2021 |url-status= live|title=Three Came Home (Full Movie) |publisher=20th Century Fox |date=20 February 1950|medium=video |time=00:12:55}}{{cbignore}}</ref> The occupation drove many people from coastal towns to the interior, fleeing the Japanese and seeking food.<ref name="Lim2008">{{cite book |author= Regina Lim |title=Federal-state Relations in Sabah, Malaysia: The Berjaya Administration, 1976–85 |url=https://books.google.com/books?id=bM4HifRARgYC&pg=PA36 |year=2008 |publisher=Institute of Southeast Asian Studies |isbn=978-981-230-812-2 |pages=36–84| via= Google Books}}</ref> The [[Malays (ethnic group)|Malays]] generally appeared to be favoured by the Japanese, although some of them faced repression, while other groups such as the Chinese and indigenous peoples were severely repressed.<ref>{{cite journal |title=The 'Slapping Monster' and Other Stories: Recollections of the Japanese Occupation (1941–1945) of Borneo through Autobiographies, Biographies, Memoirs, and Other Ego-documents |author=Keat Gin Ooi |journal=Journal of Colonialism and Colonial History |year=2006 |volume=7 |issue=3 |doi=10.1353/cch.2007.0009|s2cid=162251646 }}</ref> The Chinese were already resisting the Japanese occupation, especially with the [[Second Sino-Japanese War|Sino-Japanese War]] in mainland China.<ref>{{cite journal |jstor=20072301 |title=Anti-Japanese Activities in North Borneo before World War Two, 1937–1941 |author=Danny Wong Tze Ken |journal=Journal of Southeast Asian Studies |volume=32 |issue=1 |date= February 2001 |pages=93–105|doi=10.1017/S0022463401000042 |s2cid=162477885 }}</ref> Local Chinese formed a resistance, known as the Kinabalu Guerillas, led by [[Albert Kwok]], with broad support from various ethnic groups in northern Borneo such as [[Dusun people|Dusun]], Murut, Suluk and Illanun peoples. The movement was also supported by [[Mustapha Harun]].<ref name="Gin2010">{{cite book |author=Keat Gin Ooi |title=The A to Z of Malaysia |url= https://books.google.com/books?id=YVViEJmN99kC&pg=PA214 |year= 2010 |publisher=Scarecrow Press |isbn=978-1-4616-7199-2 |page= 214| via= Google Books}}</ref> Kwok along with many other sympathisers were, however, executed after the Japanese foiled their movement in the [[Jesselton Revolt]].<ref name= "Lim2008"/><ref>{{cite book |author=Keat Gin Ooi |title=The Japanese Occupation of Borneo, 1941–45 |url= https://books.google.com/books?id=Eg_HBQAAQBAJ&pg=PT164 |date= 2010 |publisher= Routledge |isbn=978-1-136-96309-4 |page=164| via= Google Books}}</ref>

As part of the [[Borneo campaign]] to retake the territory, [[Allies of World War II|Allied forces]] bombed most of the major towns under Japanese control, including Sandakan, which was razed to the ground. The Japanese ran a brutal [[prisoner of war]] camp known as [[Sandakan camp]].<ref>{{cite book|last=Tanaka|first=Y.|title=Hidden Horrors: Japanese War Crimes In World War II|publisher=Taylor & Francis|year=2019|isbn=978-0-429-72089-5|url=https://books.google.com/books?id=eWClDwAAQBAJ|access-date=24 January 2025|page=13}}</ref> The majority of the POWs were British and Australian soldiers captured after the [[Malayan campaign|fall of Malaya]] and [[Fall of Singapore|Singapore]].<ref>{{cite book |author1=Jane Bickersteth |author2=Amanda Hinton |title=Malaysia & Singapore Handbook |url=https://books.google.com/books?id=E5cuAQAAIAAJ |year=1996 |publisher=Footprint Handbooks |isbn=978-0-8442-4909-4}}</ref><ref>{{cite web |url=https://www.awm.gov.au/encyclopedia/pow/general_info/ |title=General information about Australian prisoners of the Japanese |publisher=[[Australian War Memorial]] |access-date=16 May 2016 |archive-url=https://web.archive.org/web/20160516160045/https://www.awm.gov.au/encyclopedia/pow/general_info/ |archive-date=16 May 2016 }}</ref> The prisoners suffered inhuman conditions, and amidst continuous Allied bombardments, the Japanese forced them to march to [[Ranau District|Ranau]], about {{Convert|260|km|mi}} away, in an event known as the [[Sandakan Death March]].<ref>{{cite web |url=https://www.awm.gov.au/exhibitions/stolenyears/ww2/japan/sandakan/ |title=World War II > Japan > Sandakan |publisher=Australian War Memorial |access-date=14 May 2016 |archive-url=https://web.archive.org/web/20160514085305/https://www.awm.gov.au/exhibitions/stolenyears/ww2/japan/sandakan/ |archive-date=14 May 2016 }}</ref> The number of prisoners were reduced to 2,345, with many of them killed en route either by [[friendly fire]] or by the Japanese. Only six of the several hundred Australian prisoners lived to see the war's end.<ref>{{cite web |url= http://www.ww2australia.gov.au/behindwire/story_marches.html |title=The Marches |work=Government of Australia |publisher=Australia's War 1939–1945 |access-date=14 May 2016 |archive-url=https://web.archive.org/web/20170315232746/http://www.ww2australia.gov.au/behindwire/story_marches.html |archive-date=15 March 2017 }}</ref> In addition, of the total of 17,488 [[Javanese people|Javanese]] labourers brought in by the Japanese during the occupation, only 1,500 survived mainly due to starvation, harsh working conditions and maltreatment.<ref name="Lim2008"/> In March 1945, Australian forces launched [[Operation Agas]] to gather intelligence in the region and launch guerrilla warfare against the Japanese.<ref name= "AWM">{{cite journal |last1=Gin |first1= Ooi Keat |title=Prelude to Invasion: Covert Operations Before the Re-occupation of Northwest Borneo, 1944–45 |journal=[[Journal of the Australian War Memorial]] |date= October 2002 |issue=37 |url= https://www.awm.gov.au/journal/j37/borneo.asp#84 |access-date=2 November 2014 |issn=1327-0141}}</ref> The [[Second Australian Imperial Force|Australian Imperial Forces]] initiated the [[Battle of North Borneo]] on 10 June 1945.<ref>{{Cite web |title=Prelude to invasion: covert operations before the re-occupation of Northwest Borneo, 1944-45 |url=https://www.awm.gov.au/articles/journal/j37/borneo |access-date=5 August 2024 |website=[[Australian War Memorial]]}}</ref><ref>{{cite book |author=Lynette Ramsay Silver |title=Blood Brothers: Sabah and Australia, 1942–1945 |url=https://books.google.com/books?id=k2ajYgEACAAJ |year=2010 |publisher=Opus Publications |isbn=978-983-3987-39-9| via= Google Books}}</ref> Japan's remaining forces surrendered on 2 September 1945, following the [[atomic bombings of Hiroshima and Nagasaki]].<ref>{{Cite book |title=A Military History of Australia |publisher=Cambridge University Press |year=2008 |isbn=978-0-511-48134-5 |edition=3rd |page=191}}</ref>

=== British crown colony ===
{{main|Crown Colony of North Borneo}}
After the Japanese surrender, North Borneo was administered by the [[British Military Administration (Borneo)|British Military Administration]] and on 15 July 1946 became a [[Crown Colony of North Borneo|British Crown colony]].<ref name="sabah edu"/><ref name="cc">{{cite news |url= http://trove.nla.gov.au/newspaper/article/95540217 |title=British North Borneo Becomes Crown Colony |page=1 |work=[[Kalgoorlie Miner]] |publisher=[[Trove]] |date=18 July 1946 |access-date=17 May 2016}}</ref> The [[Crown Colony of Labuan]] was integrated into this new colony. During the ceremony, both the [[Union Jack]] and [[Flag of the Republic of China]] were raised from the bullet-ridden Jesselton Survey Hall building.<ref name="cc"/> The Chinese were represented by Philip Lee who had been part of the resistance movement against the Japanese and who eventually supported the transfer of power to the Crown colony.<ref name="cc"/> He said: "Let their blood be the pledge of what we wish to be—[[George VI|His Majesty]]'s most devoted subjects."<ref name="cc"/>

Due to massive destruction in Sandakan during the war, Jesselton was chosen to replace the capital while the Crown continued to rule North Borneo until 1963. The Crown colony government established many departments to oversee the welfare of its residents and to revive the economy of North Borneo after the war.<ref>{{cite web |url=http://elibrary.pps-unipasby.ac.id/files/disk1/1/jtppsunipasby--ismailali-4-1-sosiohum-t.pdf |archive-url=https://web.archive.org/web/20150607141206/http://elibrary.pps-unipasby.ac.id/files/disk1/1/jtppsunipasby--ismailali-4-1-sosiohum-t.pdf |archive-date=7 June 2015 |author=Ismail Ali |title=The Role and Contribution of the British Administration and the Capitalist in the North Borneo Fishing Industry, 1945–63 |publisher=Pascasarjana Unipa Surabaya |access-date=22 April 2015 }}</ref> Upon [[History of the Philippines (1946–65)|Philippine independence in 1946]], seven of the British-controlled [[Turtle Islands, Tawi-Tawi|Turtle Islands]] (including [[Mapun, Tawi-Tawi|Cagayan de Tawi-Tawi]] and [[Mangsee Islands]]) off the north coast of Borneo were ceded to the Philippines as had been negotiated by the American and British colonial governments.<ref>{{cite news |url= https://news.google.com/newspapers?id=KhpAAAAAIBAJ&pg=5187%2C4623468 |title=Treaty over Turtle Islands |author=Charles P. Williamson |newspaper=The Telegraph |date=30 July 1929 |access-date=17 May 2016| via= Google News}}</ref><ref>{{cite news |author=Peter C. Richards |url= https://news.google.com/newspapers?nid=1301&dat=19471206&id=Sf5UAAAAIBAJ&pg=4610,725646&hl=en |title=New Flag Over Pacific Paradise |newspaper=[[The Sydney Morning Herald]] |date=6 December 1947 |access-date=22 October 2015| via= Google News}}</ref>

=== Malaysia ===
{{main|Malaysia Agreement|20-point agreement|Indonesia–Malaysia confrontation}}
[[File:Sabah during the formation of Malaysia (16 September 1963).jpg|thumb|left|[[Fuad Stephens|Donald Stephens]] (left) declaring the forming of the Federation of Malaysia at [[Merdeka Square, Kota Kinabalu|Merdeka Square]], Jesselton on 16 September 1963. Together with him was the then [[Deputy Prime Minister of Malaysia]] [[Abdul Razak Hussein|Tun Abdul Razak]] (right) and [[Mustapha Harun]] (second right).]]
On 31 August 1963, North Borneo [[Sabah Day|attained self-governance]].<ref name="tna1">{{cite web|url=http://discovery.nationalarchives.gov.uk/details/r/C10991834|title=The National Archives DO 187/31 (Declarations of independence by Sarawak, Sabah and Singapore)|publisher=[[The National Archives (United Kingdom)|The National Archives]]|year=1963|access-date=9 February 2025}}</ref><ref name="tna2">{{cite web |url=http://discovery.nationalarchives.gov.uk/details/r/C760803 |title=The National Archives DO 169/254 (Constitutional issues in respect of North Borneo and Sarawak on joining the federation) |publisher=The National Archives |date=1961–1963 |access-date=23 April 2015}}</ref><ref>{{cite book |author=Philip Mathews |title=Chronicle of Malaysia: Fifty Years of Headline News, 1963–2013 |url=https://books.google.com/books?id=md9UAgAAQBAJ&pg=PA15 |date=28 February 2014 |publisher=Editions Didier Millet |isbn=978-967-10617-4-9 |page=15}}</ref><ref>{{cite book |author=Frans Welman |title=Borneo Trilogy Volume 1: Sabah |url=https://books.google.com/books?id=glG-WBH8hkQC&pg=PA159 |access-date=28 May 2013 |publisher=Booksmango |isbn=978-616-245-078-5 |page=159|date=9 March 2017 }}</ref> The [[Cobbold Commission]] had been set up in 1962, to determine whether the people of Sabah and Sarawak favoured the proposed union of a new federation called Malaysia, and found that the union was generally favoured by the people.<ref>{{cite web |url= http://discovery.nationalarchives.gov.uk/details/r/C12304501 |title=Sarawak: Report of the Commission of Enquiry, North Borneo and Sarawak, 1962 (Cobbold Commission) |publisher=The National Archives |date=1962 |access-date=16 May 2016| via= discovery.national archives.gov.uk}}</ref> Most ethnic community leaders of Sabah, namely, Mustapha Harun representing the native Muslims, [[Fuad Stephens|Donald Stephens]] representing the non-Muslim natives, and Khoo Siak Chew representing the Chinese, would eventually support the union.<ref name="Gin2010"/><ref>{{cite book |author=Edwin Lee |title= The Towkays of Sabah: Chinese Leadership and Indigenous Challenge in the Last Phase of British Rule |url= https://books.google.com/books?id=W4QKAQAAIAAJ |year=1976 |publisher=Singapore University Press| via= Google Books}}</ref><ref>{{cite book |author=P. J. Granville-Edge |title=The Sabahan: the life & death of Tun Fuad Stephens |url=https://books.google.com/books?id=NKFuAAAAMAAJ |year=1999 |publisher=Family of the late Tun Fuad Stephens|isbn=978-983-40114-0-6 }}</ref> After a discussion culminating in the [[Malaysia Agreement]] and [[20-point agreement]], on 16 September 1963 North Borneo (as Sabah) was united with Malaya, Sarawak and Singapore, to form the independent [[Malaysia]].<ref>{{cite web |url=https://www.un.org/Depts/dpi/decolonization/trust2.htm |title=Trust and Non-self governing territories |publisher= United Nations |access-date=2 April 2016 |archive-url= https://web.archive.org/web/20110503183847/http://www.un.org/Depts/dpi/decolonization/trust2.htm |archive-date=3 May 2011 }}</ref><ref>{{cite web |url= https://www.un.org/press/en/2006/org1469.doc.htm |title=United Nations Member States |publisher=United Nations |date=3 July 2006 |access-date=1 April 2016 |archive-url= https://web.archive.org/web/20160305033119/http://www.un.org/press/en/2006/org1469.doc.htm |archive-date=5 March 2016 }}</ref>

From before the formation of Malaysia until 1966, [[Indonesia]] adopted a hostile policy towards British-backed Malaya, leading to the [[Indonesia–Malaysia confrontation]] after Malaysia was established.<ref>{{cite book |author=Bryan Perrett |title=British Military History For Dummies |url=https://books.google.com/books?id=6J6-ZD9l6bIC&pg=PA402 |date= 2007 |publisher=John Wiley & Sons |isbn=978-0-470-06191-6 |page=402| via= Google Books}}</ref> The war stemmed from what Indonesian president [[Sukarno]] perceived as an expansion of British influence in the region and his intention to wrest control over all of Borneo under the [[Greater Indonesia]]n concept.<ref>{{cite book |author=Center for Strategic Intelligence Research (U.S.) |title=A Muslim archipelago: Islam and Politics in Southeast Asia |url=https://books.google.com/books?id=tm8tSwyTa7AC&pg=PA19 |publisher=Government Printing Office |isbn=978-0-16-086920-4 |page= 19|year=2007 }}</ref> Meanwhile, the [[Philippines]], beginning with president [[Diosdado Macapagal]] on 22 June 1962, [[North Borneo dispute|claimed Sabah]] through the heirs of the Sultanate of Sulu.<ref name="PH claim">{{cite web |url=https://www.officialgazette.gov.ph/1963/01/28/philippine-claim-to-north-borneo-vol-i-i-north-borneo-claim/ |title=I. North Borneo Claim |work=Excerpt from President Diosdado Macapagal's State-of-the-Nation Message to the Congress of the Philippines |publisher=[[Government of the Philippines]] |date=28 January 1963 |access-date=17 May 2016 |archive-date=8 March 2021 |archive-url=https://web.archive.org/web/20210308124634/https://www.officialgazette.gov.ph/1963/01/28/philippine-claim-to-north-borneo-vol-i-i-north-borneo-claim/ }}</ref><ref name="PH claim research">{{cite web |url=http://www.dlsu.edu.ph/research/journals/apssr/pdf/200712/4Fernandez.pdf |title=Philippine-Malaysia Dispute over Sabah: A Bibliographic Survey |author=Erwin S. Fernandez |work= Department of Filipino and Philippine Literature, [[University of the Philippines]] |publisher=[[De La Salle University]] |date=December 2007 |access-date=17 May 2016 |archive-url=https://web.archive.org/web/20160516174241/http://www.dlsu.edu.ph/research/journals/apssr/pdf/200712/4Fernandez.pdf |archive-date=16 May 2016 }}</ref> Macapagal, considering Sabah to be property of the Sultanate of Sulu, saw the attempt to integrate Sabah, Sarawak and Brunei into the Federation of Malaysia as "trying to impose authority of Malaya into these states".<ref name="PH claim"/>

Following the successful formation of Malaysia, Donald Stephens became the first chief minister of Sabah. The first [[Yang di-Pertua Negara]] (which later changed to [[Yang di-Pertua Negeri]] in 1976) was Mustapha Harun.<ref>{{cite book |author1=Great Britain. Colonial Office |author2= Malaysia |author3=Great Britain. Office of Commonwealth Relations |title=Malaysia: agreement concluded between the United Kingdom of Great Britain and Northern Ireland, the Federation of Malaya, North Borneo, Sarawak, and Singapore |url=https://books.google.com/books?id=6gs-AQAAIAAJ |year=1963 |publisher=H. M. Stationery Off.}}</ref> The leaders of Sabah demanded that their [[freedom of religion]] be respected, that all lands in the territory be under the power of state government, and that native customs and traditions be respected and upheld by the federal government; declaring that in return Sabahans would pledge their loyalty to the Malaysian federal government. An [[Keningau Oath Stone|oath stone]] was officiated by Donald Stephens on 31 August 1964 in [[Keningau]] as a remembrance to the agreement and promise for reference in the future.<ref name="oath stone story">{{cite web |url=http://www.theborneopost.com/2010/11/30/the-story-behind-keningau%E2%80%99s-oath-stone/ |title=The story behind Keningau's oath stone |work=Bernama |publisher=The Borneo Post |date=30 November 2010 |access-date=26 August 2016 |archive-url=https://web.archive.org/web/20160825154255/http://www.theborneopost.com/2010/11/30/the-story-behind-keningau%E2%80%99s-oath-stone/ |archive-date=25 August 2016 }}</ref> Sabah held its first state election in 1967.<ref>{{cite journal |jstor=2642463 |title=Patterns and Peculiarities of Voting in Sabah, 1967 |author1=R. S. Milne |author2=K. J. Ratnam |journal= Asian Survey| date=May 1969 |volume=9 |issue=5 |pages=373–381 |doi= 10.2307/2642463}}</ref> In the same year, the name of the state capital was changed from "Jesselton" to "[[Kota Kinabalu]]".<ref>{{cite web |url=http://corporate.tourism.gov.my/mediacentre.asp?page=feature_malaysia&subpage=archive&news_id=57 |title=Sabah – Lest We Forget |publisher=Tourism Malaysia |access-date=17 June 2013 |archive-url=https://archive.today/20130801182717/http://corporate.tourism.gov.my/mediacentre.asp?page=feature_malaysia&pagemode=search&news_id=57&subpage= |archive-date=1 August 2013 }}</ref>

An [[1976 Sabah Air GAF Nomad crash|airplane crash]] on 6 June 1976 killed Stephens along with four other state cabinet ministers.<ref>{{cite news |url=http://www.therakyatpost.com/news/2015/04/05/past-air-crashes-that-involved-vips/ |title=Past air crashes that involved VIPs |author=Arfa Yunus |newspaper=[[The Rakyat Post]] |date=5 April 2015 |access-date=24 July 2015 |archive-url=https://web.archive.org/web/20150724213500/http://www.therakyatpost.com/news/2015/04/05/past-air-crashes-that-involved-vips/ |archive-date=24 July 2015 }}</ref> On 14 June 1976, the state [[government of Sabah]] led by the new chief minister [[Harris Salleh]] signed an agreement with [[Petronas]], the federal government-owned oil and gas company, granting it the right to extract and earn revenue from petroleum found in the territorial waters of Sabah in exchange for 5% in annual revenue as [[royalties]] based on the 1974 Petroleum Development Act.<ref name="KincaidShah2007">{{cite book |author1=John Kincaid |author2=Anwar Shah |title=The Practice of Fiscal Federalism: Comparative Perspectives |url=https://books.google.com/books?id=-olN8pE4tAMC&pg=PA186 |date= 2007 |publisher=McGill-Queen's Press |isbn=978-0-7735-6044-4 |page=186| via= Google Books}}</ref> The state government of Sabah ceded [[Labuan]] to the Malaysian federal government, and Labuan became a [[Federal Territory (Malaysia)|federal territory]] on 16 April 1984.<ref>{{cite web |url= http://www.dvs.gov.my/c/document_library/get_file?uuid=01e32808-0a2b-4369-9747-2021f14012c9&groupId=16746 |title= Laws of Malaysia A585 Constitution (Amendment) (No. 2) Act 1984 |work= dvs.gov.my | publisher= Department of Veterinary Services, Government of Malaysia |access-date=28 April 2014 |archive-url=https://web.archive.org/web/20140429050631/http://www.dvs.gov.my/c/document_library/get_file?uuid=01e32808-0a2b-4369-9747-2021f14012c9&groupId=16746 |archive-date=29 April 2014 }}</ref> In 2000, the state capital Kota Kinabalu was granted [[city status]], making it the [[List of cities in Malaysia|6th city in Malaysia]] and the first city in the state.<ref>{{cite news |url=http://www.dailyexpress.com.my/news.cfm?NewsID=106515 |title= Remembering Jesselton's birth |newspaper= Daily Express |date=31 January 2016 |access-date=14 May 2016 |archive-url=https://web.archive.org/web/20160514081304/http://www.dailyexpress.com.my/news.cfm?NewsID=106515 |archive-date=14 May 2016 }}</ref> Prior to a [[Ligitan and Sipadan dispute|territorial dispute]] between Indonesia and Malaysia since 1969 over two islands of [[Ligitan]] and [[Sipadan]] in the [[Celebes Sea]], the [[International Court of Justice]] (ICJ) made a final decision to award both islands to Malaysia in 2002 based on their "effective occupation".<ref name="Justice2003">{{cite book |title=Summaries of Judgments, Advisory Opinions and Orders of the International Court of Justice: 1997–2002 |url=https://books.google.com/books?id=DNoxAAAAIAAJ&q=Summaries%20of%20Judgments,%20Advisory%20Opinions%20and%20Orders%20of%20the%20International%20Court%20of%20Justice:%201997%E2%80%932002. |access-date=26 May 2013 |year=2003 |publisher=United Nations Publications |isbn=978-92-1-133541-5 |page=263 |via=Google Books }}</ref><ref name="court result">{{cite web |url= http://www.icj-cij.org/presscom/index.php?pr=343&pt=1&p1=6&p2=1 |title=The Court finds that sovereignty over the islands of Ligitan and Sipadan belongs to Malaysia |publisher=International Court of Justice |date=17 December 2002 |access-date=7 February 2016 |archive-url=https://web.archive.org/web/20140409130015/http://www.icj-cij.org/presscom/index.php?pr=343&pt=1&p1=6&p2=1 |archive-date=9 April 2014 }}</ref>

In February 2013, Sabah's [[Lahad Datu District]] was [[2013 Lahad Datu standoff|penetrated]] by followers of [[Jamalul Kiram III]], the self-proclaimed [[List of sultans of Sulu|Sultan]] of [[Sultanate of Sulu|Sulu]]. In response, Malaysian military forces were deployed to the region, which resulted in 72 deaths (56 Sultanate militants, nine Malaysian security personnel, and six civilians). Following the elimination of insurgents, an [[Eastern Sabah Security Command]] was established.<ref>{{cite news |last1=Najib |first1=Najiah |title=Lahad Datu invasion: A painful memory of 2013 |url=https://www.astroawani.com/berita-malaysia/lahad-datu-invasion-painful-memory-2013-27579 |access-date=20 April 2021 |work=[[Astro Awani]] |date=30 December 2013 |archive-url=https://web.archive.org/web/20210309203634/https://www.astroawani.com/berita-malaysia/lahad-datu-invasion-painful-memory-2013-27579 |archive-date=9 March 2021|url-status=live}}</ref><ref name="LD 2013">{{cite web |last1=Poling |first1=Gregory |last2=DePadua |first2=Phoebe |last3=Frentasia |first3=Jennifer |title=The Royal Army of Sulu Invades Malaysia |url= https://www.csis.org/analysis/royal-army-sulu-invades-malaysia |website= [[Center for Strategic & International Studies]] |access-date=20 April 2021 |archive-url=https://web.archive.org/web/20210308101424/https://www.csis.org/analysis/royal-army-sulu-invades-malaysia |archive-date=8 March 2021 |date=8 March 2013 |url-status=live}}</ref><ref name="PLD 2013">{{cite news|url=https://www.malaymail.com/news/malaysia/2019/02/25/after-six-years-police-commandos-shed-light-on-lahad-datu-incursion/1726688|title=After six years, police commandos shed light on Lahad Datu incursion|last=Bunyan|first=John|work=Malay Mail|date=25 February 2019|access-date=24 January 2025|quote=The Lahad Datu standoff reportedly saw a total of 68 deaths, including 56 from the Sulu sultanate, nine from the Malaysian authorities and six civilians.}}</ref>