I am sharing a timeline I have compiled of key events and accompanying literature on the North Borneo (Sabah) issue. This timeline is being shared for academic and media research purposes. It is not being published as an official statement of policy in any shape or form, nor does this timeline purport to be representative of of the views of the Philippine government.
Spain signed peace treaties with the strongest sultanates, Sulu and Maguindanao, recognizing their de facto independence.
Sultan of Sulu became sovereign ruler of most of North Borneo by virtue of a cession from the Sultan of Brunei whom he had helped in suppressing a rebellion.
There is no document stating the grant of North Borneo from Sultan of Brunei to Sultan of Sulu, but it is accepted by all sides.
March 17, 1824
Treaty of London signed by the Netherlands and Great Britain
Allocates certain territories in the Malay archipelago to the United Kingdom and the Netherlands (Dutch East Indies).
September 23, 1836
Treaty of Peace and Commerce between Spain and Sulu, signed in Sulu
Granting Spanish protection of sultanate, mutual defense, and safe passage for Spanish and Joloan ships between ports of Manila, Zamboanga, and Jolo.
Ortiz: Spain did not claim sovereignty over Sulu, but merely offered “the protection of Her Government and the aid of fleets and soldiers for wars…”
Muda Hassim, Uncle of the Sultan of Sulu, publicly announced as successor to the Sultanate of Sulu with the title of Sultan Muda: he was also the leader of the “English party,”(today the term for Crown Prince is Raja Muda)
The British Government appoints James Brooke as a confidential agent in Borneo
The British Government extends help to Sultan Muda to deal with piracy and settle the Government of Borneo
Sir James Brooke receives intelligence that the Sultan of Sulu ordered the murder of Muda Hassim, and some thirteen Rajas and many of their followers; Muda Hassim kills himself because he found that resistance is useless. 
July 19, 1846
Admiral Thomas Cochrane, Commander-in-chief of East Indies and China Station of the Royal Navy, issued a Proclamation to cease hostilities (“piracy,” crackdown versus pro-British faction) if the Sultan of Sulu would govern “lawfully” and respect his engagements with the British Government
If the Sultan persisted, the Admiral proclaimed that the squadron would burn down the capital of the sultanate.
May 7, 1847
James Brooke is instructed by the British Government to conclude a treaty with the Sultan of Brunei
British occupation of Labuan is confirmed and Sultan concedes that no territorial cession of any portion of his country should ever be made to any foreign power without the sanction of Great Britain
May 29, 1849
Convention of Commerce between Britain and the Sultanate of Sulu
Sultan of Sulu will not cede any territory without the consent of the British. 
April 30, 1851
Treaty signed with Spain by the Sultan of Sulu, Mohammed Pulalun
The Sultanate of Sulu was incorporated into the Spanish Monarchy.
January 17, 1867
that, whatever Treaty rights Spain may have had to the sovereignty of Sulu and its dependencies, those rights must be considered as having lapsed owing to the complete failure of Spain to attain a de facto control over the territory claimed.
May 30, 1877
Protocol of Sulu signed between Spain, Germany, and Great Britain, providing free movement of ships engaged in commerce and direct trading in the Sulu Archipelago
British Ambassadors in Madrid and Berlin were instructed that the protocol implies recognition of Spanish claims over Sulu or its dependencies.
At this point the following western countries have possessions in Southeast Asia:
1. British = Singapore, Malaya, Brunei, Sarawak, and North Borneo
2. Germany = Papua New Guinea
3. Netherlands = Indonesia
4. Spain = Philippines, Guam, Marshall Islands, Caroline Islands
5. France = Vietnam, Laos, Cambodia (French IndoChina)
Expeditions of Alfred Dent to control north part of Borneo began
Alfred Dent, member of the commercial house of Dent Brothers and Co. of London 
January 22, 1878
Sir Alfred Dent obtains sovereign control over the northern part of Borneo for 5,300 ringgit ($5,000) from the Sultans of Brunei and Sulu. See contending translations of relevant portions of this document. See also the Spanish translation. See another English translation.
Concessions would later be confirmed by Her Majesty’s Royal Charter in November, 1881 granted to the British North Borneo Co.
The territory of the Sultan of Sulu over the island of Borneo,
commencing from the Pandassan River on the north-west coast and extending along the whole east coast as far as the Sibuco River in the south and comprising amongst other the States of Paitan, Sugut, Bangaya, Labuk, Sandakan, Kina Batangan, Mumiang, and all the other territories and states to the southward thereof bordering on Darvel Bay and as far as the Sibuco river with all the islands within three marine leagues of the coast. 
Sultan of Sulu Mohammed Jamalul Alam appoints Baron de Overbeck as Datu Bendajara and Raja of North Borneo