I believe that our country, the Philippines, really owns Sabah and here is the timeline to trace the history of this issue.
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
Earl of Derby to Lord Odo Russel:
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.
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.
November 1, 1881
Queen Victoria grants Charter of Incorporation to the British North Borneo Company
British North Borneo Company now does actually exist “as a Territorial Power” and not “as a Trading Company”
November 16, 1881
Spaniards protest granting of Royal Charter
By virtue of treaties of capitulation of 1836, 1851, and 1878, Spain exercised sovereignty over Sulu and its dependencies including North Borneo; Sultan of Sulu had no right to enter into any treaties or make any cessions whatsoever 
January 7, 1882
British Foreign Minister Earl Granville’s letter says Crown assumes no dominion or sovereignty over the territories occupied by the Company, nor does it purport to grant to the Company any powers of Government thereover.
March 7, 1885
Spanish claims to Borneo abandoned by Protocol of Sulu entered into by England, Germany and Spain
Spanish supremacy over the Sulu Archipelago was recognised on condition of their abandoning all claim to the portions of Northern Borneo which are now included in the British North Borneo Company’s concessions.
May 12, 1888
While civil war was ongoing in Sulu.
An agreement between the British North Borneo Company and Great Britain; British Government admits the North Borneo Company derived its rights and powers to govern the territory.
June 14, 1888
British Protectorate established over Sarawak.
September 17, 1888
British Protectorate established over Brunei.
December 10, 1898
Spain cedes the Philippine Islands to the United States of America. The treaty lines did not include North Borneo (Sabah).
President Aguinaldo invites the Sultan of Sulu to join the newly-established First Republic of the Philippines.
Malolos Congress appointed representatives for Jolo: Benito Legarda and Victor Papa.
August 20, 1899
Treaty acknowledged the “sovereignty of the United States over Jolo and its dependencies”
April 28, 1950
House of Representatives approved Concurrent Resolution No. 42 expressing the “sense of the Congress of the Philippines that North Borneo belongs to the heirs of the Sultan of Sulu and the ultimate sovereignty of the Republic of the Philippines and authorizing the President (Elpidio Quirino) to conduct negotiations for the restoration of such ownership and sovereign jurisdiction over said territory.” The Senate did not approve the Resolution.
Reps. Macapagal (Pampanga), Rasul (Mindanao and Sulu), Escarreal (Samar), Cases (La Union), Tizon (Samar), Tolentino (Manila), and Lacson (Manila) author the Resolution.
September 4, 1950
Philippines advised British Government that a dispute regarding ownership and sovereignty over North Borneo existed between the two countries.
August 30, 1955
Vice President Carlos P. Garcia and the British Ambassador to Manila signed an agreement that provided for the employment and settlement of 5,000 skilled and unskilled Filipino agriculturists and miners in North Borneo
Agreement not implemented as North Borneo employers feared multiple suits arising from claims of Filipino laborers: they had found a sizable number of Indonesians willing to work on a temporary basis.
Governor of North Borneo visits Manila to implement the 1955 labor treaty.
500-man delegation of Filipino Muslims present resolution to President Ramon Magsaysay calling for direct negotiations with the British to return North Borneo to the Philippines. Magsaysay did not act on the resolution.
British response: United Kingdom High Commissioner for Southeast Asia said it would not take seriously the demands of Moros in the Philippines for certain areas of North Borneo.
July 31, 1957
The Federation of Malaya Act was signed.
The Federation of Malaya was established as a sovereign country within the British Commonwealth.
November 25, 1957
Muhammad Esmail Kiram, Sultan of Sulu, issued a proclamation declaring the termination of the Overbeck and Dent lease, effective January 22, 1958.
“A syndicate headed by Nicasio Osmeña acting as attorney-in-fact for the heirs, attempted without success to negotiate with the British Foreign Office for a lump sum payment of $15 million in full settlement of the lease agreement.”
August 31, 1957
Peninsular Malaya granted independence by Britain.
May 27, 1961
Inclusion of North Borneo (Sabah) in the concept of Malaysia after the UK talks
It was during this time when then President Diosdado Macapagal was forced to initiate the filing of the Philippine claim in North Borneo (Sabah) as it was being considered as a member of the proposed concept of Malaysia broached by Prime Minister Tengku Abduk Rahman in Singapore.
February 5, 1962
Attorneys of the heirs of the Sultan of Sulu wrote to the Department of Foreign Affairs with the desire to have the territory included as part of the national territory of the Republic of the Philippines;
Ortiz: J.C. Orendain, acting as counsel for the heirs – regain proprietary rights to North Borneo and that sovereignty be turned over to the Philippine Republic.
April 24, 1962
Heirs of the Sultan of Sulu ceded sovereignty rights over Sabah to the Philippine Government.
Resolution No. 321 unanimously adopted by House of Representatives, urging President Macapagal to take the necessary steps for the recovery of North Borneo (Sabah).
Filed by Rep. Godofredo Ramos (Aklan) the resolution read: “It is the sense of the House of Representatives that the claim to North Borneo is legal and valid.”
September 11, 1962
President Diosdado Macapagal issues special authorization in favor of Vice President Emmanuel Pelaez to formally accept, on behalf of the Republic of the Philippines, the cession or transfer of sovereignty over the territory of North Borneo by Sultan Mohammad Esmail Kiram, Sultan of Sulu.
September 12, 1962
Heirs of the Sultan of Sulu cede all rights, proprietary, title, dominion and sovereignty to the Republic of the Philippines
Secretary of Foreign Affairs sends Note to British Ambassador asserting that the Philippine claim subsists despite the London agreements including North Borneo in the Federation of Malaysia.
September 27, 1962
Vice-President Emmanuel Pelaez addresses the United Nations General Assembly
We stand on what we consider to be valid legal and historical grounds. Our claim has been put forward with sincere assurance of our desire that the issue be settled by peaceful means, and without prejudice to the exercise of the right of self-determination by the inhabitants of North Borneo, preferably under United Nations auspices.
June 7 – 11, 1963
Discussion between the foreign affairs secretaries of the Federation of Malaysia, Indonesia, and the Philippines.
The meeting resulted in the drafting of the Manila Accord.
July 9, 1963
Malaysia Agreement was signed.
Article I provided for the creation of the Federation of Malaysia which included the colonies of Singapore, North Borneo, and Sarawak.
July 30 – August 5, 1963
MAPHILINDO (Malaya, Philippines, Indonesia) is formed, a loose consultative body among the three countries.
July 31, 1963
Manila Accord is signed
Indonesia, the Federation of Malaya, and the Philippines sign a policy statement agreeing to peacefully resolve the issue on North Borneo.
July 14-16, 2004
JCBC discusses Filipino workers in Sabah and proposes Philippines set up a consulate in Sabah.
The Malaysian side requested the Philippine side to establish a Consulate in Sabah as soon as possible. The Philippine side reiterated the government’s commitment on this matter.
September 14, 2004
Executive Order No. 357 The Bipartisan Executive-Legislative Advisory Council on the Sabah Issues was abolished and its functions transferred to DFA
Group calling itself the “Royal Sultanate of Sulu Archipelago’s Supreme Council” warned Malaysian government not to entertain claims forwarded to it by so-called Sultan Rodinood Julaspi Kiram regarding the resolution of the North Borneo territorial issue.
April 27-28 2006
Closing Statement of Malaysian Foreign Minister Dato’ Seri Syed Hamid Albar at the 6th Malaysia-PH Joint Commission Meeting
Malaysian Foreign Minister Dato’ Seri Syed Hamid Albar, in his closing statement during the 6th Malaysia-PH Joint Commission Meeting in Kuala Lumpur, asked Secretary Alberto G. Romulo to jointly “find ways to bring a final conclusion to the long due bilateral matters, namely the displaced people in Sabah and the setting up of the Philippine Consulate General in Kota Kinabalu.”
June 3, 2006
Mohammad Fuad Abdulla Kiram I was proclaimed 35th Sultan of the Royal Hashimite Sultanate of Sulu and Sabah with a backing of the Moro National Liberation Front.
Jamalul Kiram III runs unsuccessfully for Senator under Partido Demokratikong Sosyalista ng Pilipinas (PDSP), receiving over two million votes. PDSP coalesces with President Gloria Macapagal-Arroyo’s Lakas-CMD and KAMPI to form TEAM Unity. Administration coalition is crushed in the polls with only two of its bets winning, the other 10 seats are won by the opposition.
Introduced by Hon. Antonio V. Cuenco
May 29, 2008
Nur Misuari called for the revival of North Borneo claim in Second Mindanao Leadership Summit attended by MNLF combatants
Strong reaction from Datuk Seri Panglima Yong Teck Lee, President of the Sabah Progressive Party urging Malaysia’s Federal Government to bring in military, set up consulates in Mindanao and invite PHL to set up consulate in Sabah
July 9, 2008
“Sultanate of Sulu” reportedly starts issuing birth certificates to Filipinos in Sabah
July 27, 2008
Datu Omar negotiator of Mohammad Jamal Al Alam heirs was quoted “obtained signatures of nine heirs relinquishing claims to Sabah” but these are denied by claimants
Uka Ulama claimed that nobody has the power to drop the claim because there is no more Sultan who reigns and rules over the territory.
August 10, 2008
Sulu provincial government tells Malaysia to Increase annual payment to Jamalul Kiram III to $500M.
August 20, 2008
President Gloria Macapagal-Arroyo issues Memorandum Circular No. 162 or “Guidelines on matters pertaining to North Borneo (Sabah)”
No recognition of a foreign state’s sovereignty over North Borneo; any official activity relating to North Borneo carried out only with the clearance of or after consultations with DFA
March 10, 2009
President Gloria Macapagal-Arroyo signs R.A. 9522, amending R.A. 5446
In fulfilment of the second Malaysian stipulation, President Gloria Macapagal-Arroyo removes mention of Sabah or North Borneo in the Archipelagic Baselines of the Philippines law
Nur Misuari issued a statement calling the attention of Malaysia to settle the Sabah issue.
Sulu provincial board passed a resolution supporting the demand of heirs to increase the yearly payment to at least $500 Million. 
July 16, 2011
Supreme Court decision (GR No. 187167) upholds the baseline law
In its decision, the Supreme Court makes a conclusion of law: that R.A. 9522 did not repeal R.A. 5466, and that therefore, the Philippine claim over Sabah is retained and can be pursued. However, since this is a conclusion of law, the Supreme Court made its conclusion of law without explaining the reasons for its conclusion. It makes the decision, however, binding on the government.
April 24-27, 2012
Visit to the Philippines of Malaysian House Speaker Pandikar Amin Haji Mulia
Malaysian House Speaker Pandikar Amin Haji Mulia raised the matter of the opening of a consulate during his call on President Benigno S. Aquino III, who, in response, instructed the Secretary of Foreign Affairs to study the proposal.
June 5, 2012
Upon returning from a visit to Malaysia, Vice-President Binay says he will recommend to the President the setting up of a Philippine Consulate in Sabah.
February 12, 2013
Followers of Jamalul Kiram numbering over 200 men landed in Laha Datu village in Sabah on February 12, 2013.
Seriously, this issue is stressing me out!! I continue to believe that the Philippines have alegitimate claim to Sabah. The fact that Malaysia is paying more than 7000 ringgitsannually to the heirs of the Sultan of Sulu until now, clearly showed that theyrecognize who the rightful owners of Sabah are! How could they lay claim to a territory when they are paying rent to Filipino citizens? You don’t have to be a lawyer to figure out that this part of Borneo is legally our turf.
Over the years, several hundred thousand Filipinos were forced out of Sabah, but the present dispensation have not dared to raise even a sigh of protest to this ruthless act against our compatriots. I am not sure why our dear leaders would not dare to antagonize this nation. They prefer to be bullied than asserting the rights of the affected Filipinos in exchange for what, economic ties?
It is very clear that Sabah is very much part of our country and its history. Malaysian government is pathetic. Nothing more, nothing less.
“Short History of the Sulu Sultanate.” Sovereign Sulu. N.p., n.d. Web. 21 Feb. 2013. <sovereignsulu.webs.com/Short%20History-Sulu%20Sultanate.pdf>.
British North Borneo. “British Borneo Treaties.” Lawnet. N.p., n.d. Web. 21 Feb. 2013. <www.lawnet.sabah.gov.my/Lawnet/SabahLaws/Treaties/GrantBySultanOfSuluOfTerritoriesAndLandsOnTheMainlandOfTheIslandOfBorneo.pdf>.
“Hadji Rodinood M. Sultan Julaspi Kiram – reigning 29th Sultan of Sulu.” Sovereign Sulu. N.p., n.d. Web. 23 Feb. 2013. <sovereignsulu.webs.com/>.
“History of the Royal House of Sulu.” Official website of the Royal House of Sulu. N.p., 20 Dec. 1936. Web. 22 Feb. 2013. <http://www.royalsultanateofsulu.org/#!history>.