Only about 15 million years ago did the island of Borneo really begin to push its way out of the sea, although some parts of what is now eastern Sabah may have appeared above the surface of the sea during the Cretaceous period (140 million to 65 million years ago). The large limestone massifs found mainly on the east coast of Sabah were formed during this period and may have emerged and submerged many times, most recently 2 million years when they re-emerged. During the Pleistocene period about 2.5 million years ago, Borneo, Java, Sumatra, Celebes and Peninsula Malaysia were all joined together, along with many smaller islands and they formed a continent known as Sundaland. At times when the sea level was low they were all connected to mainland Asia and it would have been possible to walk from here to Ireland without crossing sea. This ancient land bridge had the effect of enriching the flora and fauna of Borneo. The seas rose again separating Sundaland, leaving Borneo to evolve separately.
During the Miocene period, 10 to 15 million years ago, a large mass of molten rock intruded beneath the marine sediments that were eventually to form the Crocker Range of mountains. The rock cooled, hardened and formed granite. This granite pluton remained buried beneath the earth's surface until just over a million years ago, when it forced its way upwards at a geologically tremendous rate to form Mount Kinabalu.
The island of Borneo found its present coast line only about 10,000 years ago as the gigantic blocks of ice formed during the last ice age melted away and raised the sea level.
The prehistory of Sabah is most interesting, in fact unique in South East Asia. The oldest sites are found in Tingkayu area near Kunak, on the east coast of Sabah. These sites, around the shore of a prehistoric lake, formed by a lava flow blocking the Tingkayu river more than 30,000 years ago provide evidence of main activities 31,000 years ago. The stone tools produced at this, what is believed to be a factory (manufacturing) site are some of the finest found in South East Asia. Similar stone tools found in other areas of South East Asia date back 17,000 to 20,000 years ago, meaning to say, man in Sabah was 10,000 years more advanced than any other man so far discovered in South East Asia. If this was a factory site, and all evidence points to this fact, then specialization of work already existed 30,000 years ago; specialization also means trade. But these early Sabahans were not the forbears of modern day Sabahans, they were probably more akin to the present day Australian Aborigines. The forbears of modern Sabahans, that is, the Mongoloid Kadazan, Dusun, Murut, Orang Sungai etc. only arrived on these shores about 5,000 years ago.
Tingkayu lake drained away about 15,000 years ago further exposing the limestone massif at its centre. In the caves shelthers of this limestone massif, known as 'Baturong', evidence of man around the time of the lake's disappearance has been found. Man inhabited Baturong and the cave sites at Madai, a few miles away, from about 15,500 years ago until 6,500 years ago. But the skillfully made stone tools from Tingkayu 15,000 years earlier had disappeared. The technology was lost. We are still not sure if the inhabitants of Madai and Baturong were the descendents of the Tingkayu peoples. If they were, why were the skills lost? If not, what happened to those people? One possible answer is that they were defeated by a stronger more numerous rations. But why were the skills not passed on? Could they have been wiped out completely? We don't know.
From 6,000 years ago until 2,500 years ago we have found no evidence of man in the cave sites, but it was during this time that the first Mongoloid settlers arrived. Evidence of this is found in the stone tools and potteries discovered at Bukit Tengkorak near Semporna. Also the obsidian drill bits found here do not come from Sabah. The nearest source is a few South Sea Islands. This suggests long distance migration. About 2,500 years ago man moved back to Madai and Baturong. There is an abundance of potteries of the late neolithic material. The materials of Bukit Tengkorak however seem to predate the Madai late neolithic and could possibly date back to 4,000 to 5,000 years before present. As yet carbon dating is not completed. But this site being on the coast, could be one of the early Mongoloid settlements. Two teeth found at the site have proved to be the teeth of Mongoloid peoples.
From 2,000 to 1,000 years ago finds from the caves are characterised by rich incised potteries, copper and bronze artifacts and iron (Madai iron spears).
From 1,000 to 500 years ago finds are characterised by burial coffins and also burial jars. Burial jars during this period are found all across Sabah, not only in caves but also beneath the ground.
About 500 years ago people ceased permanent habitation in the caves although they continued to be and still are seasonally occupied for the collection of bird nests, which are used for the Chinese delicacy, Bird's Nest Soup. The first mention of nest collection is in 1761, from Madai, in the annals of the Sultanate of Sulu, although they were probably collected before this as the Chinese had been trading along the coasts of Borneo since about 700 A.D.
It is known that as long ago as 700 A.D. trade and diplomatic links of some form existed between Borneo and China. In 1406 according to Chinese records the Rulers of Brunei sent an envoy to China with gifts for the Chinese Emperor. Also recorded in Chinese annals is the existance of a Chinese principality established somewhere along the Kinabatangan River. Exactly where has not yet been discovered. The Kinabatangan is a large river and would have been navigable by what were sea-going ships in those days for at least 50 to 60 miles. The settlement could have been on either bank. By now it will probably be covered with at least 10 to 20 feet of silt, if not more, as the river overflows its banks every year.
It is also known from the records that some time in the 15th Century a Chinese princess from the Kinabatangan married the first Sultan of Brunei, the term Sultan only being used after Brunei, converted to Islam and became the second Sultan.
But basically before the 16th century the area we now know as Sabah, Brunei and Sarawak centred around the kingdom of a Brunei, Brunei being the centre for trade with China. This region was in turn controlled by two great empires of that period; first the Sri Vijayan of Sumatra and then by Majapahit of Java. However in the early 15th century the Malacca empire spread its influence and took over the trade of Brunei. Through its traders Islam spread to Brunei and the leadership of the Islamic faith in South East Asia passed to the Brunei Sultans after the fall of Malacca to the Portuguese in 1511. Under Sultan Bolkiah, Brunei extended its influence over the greater part of Borneo and as far north as Luzon and Sulu but internal quarrelling in the Brunei Sultanate in the 1600s was one of the factors that led to the decline of the empire.
No other foreigners, who had dealings with Borneo, with the exception of the Europeans, left any written records of their activities.