Filipino rebels had already defeated the Spanish except those in the walled city of Intramuros within Manila. They believed American forces had come to help solidify their independence from Spain, but the United States Government wanted the Philippines. Americans and Filipinos became entangled in a bloody guerrilla war.
To prevent aid to Filipino forces in 1901, U.S. forces locked the entire population of the province of Batangas into camps under command of a vindictive leadership, where normal death rates tripled. The Americans did not know who was a 'rebel' and who wasn't or who helped them. But civilians were threatened by the 'rebels' if they did not aid them. The Americans called the camps 'reconcentration camps', and they were essentially the very same type of concentration camps brutally used by Spain in Cuba and causing the U.S. to declare war on Spain in 1898 in the first place. The general in charge of the Batangas camps made it clear he would make the residents/inmates (guilty and innocent alike) pay for helping the Filipino fighters and no longer desire for the fighting to go on (as if they did).
After Spain left, the Philippine Islands needed American protection but not the brutal conquest they received: 4000 American combat dead, 15,000 Filipino combat dead, at least 150,000 Filipino civilian deaths with estimates as high as 600,000. The truth is probably around 250,000 civilian dead from starvation, disease, American gunfire and naval bombardments, and some torture and executions. As in any war there were rapes, and this one offered a few outrageous reports. One particularly immoral and heinous gang rape reported by a corporal who claimed to have witnessed it is in the Congressional record. He was discredited by prowar legislators, and no one may ever know if his tale was true. The incident is related in several recent histories of he Philippine American War, and I have read the testimony in the Congressional Record.