Philippines Nationalist had begun a rebellion against Spanish rule in 1896. When the United States took control in 1899 they continued the rebellion. The result, a war that lasted until 1913. 4,200 US soldiers died as did 20,000 rebels up to 200,000 Philipino civilians died as well.
On July 7, 1892, Andres Bonifacio began a revolutionary movement to gain independence from Spain. The rebels initially made progress against the Spanish, but the Spanish soon gained the upper hand. The Rebel leader who had become Emilio Aguinaldo left the country after receiving a payoff from the Spanish. After a brief stay in exile, Aguinaldo returned at the same time Admiral Dewey was defeating the Spanish fleet. His forces quickly captured most of the island and surrounded Manila. Aguinaldo claimed that he had received assurances from both US consul in Singapore and from Admiral Dewey that the US would give the Philippines independence once it had been liberated from the Spanish. Dewey denied that promised stating :
"From my observation of Aguinaldo and his advisers I decided that it would be unwise to co-operate with him or his adherents in an official manner. ... In short, my policy was to avoid any entangling alliance with the insurgents, while I appreciated that, pending the arrival of our troops, they might be of service.”
The United States had reached an agreement that the Spanish forces would surrender to US forces and not to the rebels, which they did after the US captured Manila on August 13th.
The question then was what to do with the Philippines- President McKinley stated "We could not leave them to themselves- they were unfit for self-government, and they would soon have anarchy and misrule over there, worse than Spain's was... [and] there was nothing left for us to do but take them all, and educate the Filipinos and uplift and Christianize them."
Thus McKinley issued the Proclamation of Benevolent Assimilation. The Philippino’s felt betrayed. Aguinaldo protested "most solemnly against this intrusion of the United States Government on the sovereignty of these islands."
Actual warfare between the sides began on February 4th, 1899 when an American sentry shot and killed two Philippine soldiers. Clashes broke out, and the next day the US started an all-out assault on Philipino troops. For the first year of the war, the Philippines tried to deploy conventional forces against the Americans hoping that if they could inflict enough casualties, the Americans would decide it was not worth the fight. The Philippino’s could not sustain that type of warfare against a better equipped American force, and after McKinley was reelected, they transitioned to Guerrilla Warfare. The American troops captured Aguinaldo on March 23, 1901, and a few days later he swore allegiance to the Americans and called on his supporters to lay down their weapons. The war continued with General Miguel Malvar leading the opposition; he too was captured on April 16, 1902. The war came to an official end when the Philippine Organic Act was passed. It gave the Philippines limited self-rule and extended the protection of the Bill of rights to the Philippines.