Other groups, including the Moro, Bicol and Pulahan peoples, continued hostilities in remote areas and islands, until their final defeat at the Battle of Bud Bagsak on June 15, 1913.

During the Spanish–American War, Emilio Aguinaldo (who had led an unsuccessful insurrection against Spain in 1896–97) organized a native army in the Philippines and secured control of several islands, including much of Luzon.

Cession of the Philippines to the United States on December 10, 1898 via the Treaty of Paris disappointed many Filipinos, and on February 4, 1899 Aguinaldo's followers clashed with American troops.

The Americans, numbering about 12,000 combat troops under Major General Elwell Otis, defeated Aguinaldo's force of some 40,000 men and suppressed an attempted uprising in Manila.

[Note 1] American columns pushed north, east, and south from Manila to split the insurgent forces and seize key towns.

[18] The column pushing south, commanded by Brigadier General Henry Lawton, was tasked with a long raid along Laguna de Bay; its mission assignment was limited because of manpower shortages due to primacy of the northern theater.

Frank F. Wilde's naval squadron, took Iloilo from Filipino forces under General Martin Delgado, Panay's Federal State of the Visayas, and Ananias Diokno, leaving the city a "blackened ruin".

Gen. James F. Smith arrived Bacolod on 4 March as the Military Governor of the Sub-district of Negros, after receiving an invitation from the president of the provisional government, Aniceto Lacson.

[27] At Calumpit, where Luna's main force was located, thousands of laborers had strengthened the formidable natural defenses with trenches roofed by steel rails or boilerplate for protection from shrapnel and the construction of breastworks at several points.

[28] Luna had deployed much of his army along the railway line south of Calumpit, and on the night of April 10–11 he launched a series of assaults on garrisons along the railroad, driving the Americans back but failing to rout them.

[31] On May 2, Aguinaldo's representatives proposed a three-month cease-fire, couched in language which required Otis to acknowledge the Philippine Republic as a sovereign nation.

Otis refused the truce on those terms, but gave the delegate a copy of President McKinley's plan for a Philippine civil government, which would include an advisory council and judiciary selected from Americans and Filipinos.

The result of such meeting has been the election of señor Francisco Guerrero, who is therefore announced as Mayor and authorized to select a council and such other assistants or officers as may be necessary to properly administer municipal affairs.

[Note 1] Following the murder of Luna, Aguinaldo had about 4,000 soldiers, mostly located along the Manila-Dagupan railroad, under the command of Tomas Mascardo, Servillano Aquino and Luciano San Miguel in Pampanga; Pio del Pilar and Urbano Lacuna in Bulacan, Francisco Macabulos in Tarlac; Gregorio del Pilar in Pangasinan; Manuel Tinio in Ilocano; and Daniel Tirona in the Cagayan Valley.

[51] The navy used 25 seagoing gunboats, complementary to the army's 10 river steamers, which were armed with cannons and machine guns, and stationed them at Zamboanga, Cebu, Iloilo and Vigan.

Perhaps as a diversion, Filipino forces south of Manila had attacked Calamba and Los Baños in Laguna and Imus and Bacoor in Cavite in late 1899.

[55] Young pressed northeast towards Cabanatuan, Nueva Ecija, a city reputed to hold two dozen American and 4,000 Spanish prisoners of war, advancing slowly over difficult terrain.

[59] Though hampered by a typhoon which caused rivers to rise ten feet and washed out roads, the forces entered the town of Tarlac on November 12.

[57] Recognizing that American troops blocked his escape east, Aguinaldo turned north and west on November 15, crossing the mountains into La Union province.

[69] With permission from Lawton, Young proceeded north from Cabanatuan on 7 November with an 1,100-man cavalry brigade, towards Tayug, Pangasinan, intending to block Aguinaldo's escape route.

[70] Aguinaldo's escape north from Pozorrubio should have been blocked by a force under General Wheaton which had left Manila by sea on November 6 and arrived in San Fabian, Pangasinan the next day.

After being notified by a rider of the outcome of the battle and the death of Del Pilar, Aguinaldo ordered that camp be broken, and departed with his party for Cayan settlement.

[77] Maj. Gen. Pantaleon Garcia, revolutionary commander of Central Luzon, was captured in May 1900, while Gen. Servillano Aquino, Francisco Macabulos, and Pio del Pilar surrendered in June.

[85] On March 23, 1901 General Frederick Funston and his troops captured Aguinaldo in Palanan, Isabela, with the help of some Filipinos (called the Macabebe Scouts after their home locale[86][87]) who had joined the Americans' side.

[88] On April 1, 1901, at the Malacañan Palace in Manila, Aguinaldo swore an oath accepting the authority of the United States over the Philippines and pledging his allegiance to the American government.

"The lesson which the war holds out and the significance of which I realized only recently, leads me to the firm conviction that the complete termination of hostilities and a lasting peace are not only desirable but also absolutely essential for the well-being of the Philippines.

"[90][91] Not all of the insurgent leaders had responded to Aguinaldo's acceptance of the United States authority and his call for an end to the fighting, but by July 1901 only Miguel Malvar in Batangas and Vincente Lukban in Samar still led forces capable of resisting American control.

[94] His official issuance, however, was a proclamation of general amnesty for persons who had participated in or supported Philippine insurrections against the U.S., and explicitly excluded parts of the territory "inhabited by Moro tribes".

When the Army occupied former Spanish garrison points, the Moros began to raid villages, attack soldiers, and otherwise resist American jurisdiction.

In May 1905, March 1906, and June 1913, Regulars had to cope with disorders too extensive to be handled by the local constabulary and Philippine Scouts on the island of Jolo, a Moro stronghold.