While McKinley accepted congratulations on ratification of the treaty, the reaction in the Philippines was less enthusiastic. Indeed, two days before the Senate voted, Aguinaldo had again taken up the fight for independence. This time it was the Americans rather than the Spanish who stood in the way, and it was the Americans rather than the Spanish who were charged with committing atrocities in a long, bloody guerrilla war. American forces eventually captured Aguinaldo in March 1901, and by 1902 his insurrection had been crushed. The rebellion in the Philippines had turned out to be much more costly in both lives and dollars than the Spanish-American War itself.
The Philippine Insurrection was but the first of many difficulties that were to confront the United States in distant parts of the world after the Spanish-American War. Victory brought to the McKinley administration responsibility for establishing orderly government in the newly acquired possessions. To the administration came, as well, responsibility for perfecting a foreign policy to guide the United States in the intricate diplomatic maneuvering that took place at the turn of the century. As he wrestled with the problems of policy formation, McKinley came to rely heavily on two new members of his cabinet: John Hay, who assumed office as secretary of state on 30 September 1898, and Elihu Root, who replaced Alger as secretary of war on 24 July 1899.
With governmental arrangements for the former Spanish colonies entrusted to the Department of War, Root immediately set his orderly mind to the task of working them out. His recommendations included removal of tariff barriers between Puerto Rico and the United States so as to promote economic development and "avoid trouble in the island." Although Congress, in 1900, considered a bill to carry out the recommendation, its free-trade provisions offended supporters of tariff protection. A compromise bill then restored a tariff, albeit with reduced rates. It also provided that all duties should cease when a new civil government's system of taxation had become operative. Congress passed the bill, and McKinley signed it on 12 April 1900. Civil government for the island was established on 1 May, and a legislative assembly convened on 3 December. McKinley issued a proclamation removing the tariff on 25 July 1901.
Turning to Cuba, Root insisted that its new constitution include the Platt Amendment, which gave the United States the right to intervene in Cuban affairs, bound Cuba to avoid commitment to another power, and imposed limitations on the size of the Cuban national debt. Though Cubans always resented the intrusion on their national sovereignty, Americans hailed Root's program as a model of efficiency. The military governor under Root's direction, General Leonard Wood, achieved physical, medical, and educational improvements to benefit the island and create a stable regime. In the Philippines, Root acted to strengthen the army, subdue the rebellion, and establish political institutions through the supervision of an American commission. To set the Philippine government on a solid base, McKinley in 1900 selected William Howard Taft as commissioner. It was Taft, acting on instructions from Root, who guided the transition from military to civilian government.