For McKinley's stated intentions for the Philippines, most people start from this interview of him published 1903:

When next I realized that the Philippines had dropped into our laps, I confess I did not know what to do with them. I sought counsel from all sides--Democrats as well as Republicans--but got little help. I thought first we would take only Manila; then Luzon; then other islands, perhaps, also.

I walked the floor of the White House night after night until midnight; and I am not ashamed to tell you, gentlemen, that I went down on my knees and prayed to Almighty God for light and guidance more than one night. And one night late it came to me this way--I don't know how it was, but it came:

(1) That we could not give them back to Spain--that would be cowardly and dishonorable;

(2) That we could not turn them over to France or Germany, our commercial rivals in the Orient--that would be bad business and discreditable;

(3) That we could not leave them to themselves--they were unfit for self-government, and they would soon have anarchy and misrule worse then Spain's was; and

(4) That there was nothing left for us to do but to take them all, and to educate the Filipinos, and uplift and civilize and Christianize them and by God's grace do the very best we could by them, as our fellow men for whom Christ also died.

And then I went to bed and went to sleep, and slept soundly, and the next morning I sent for the chief engineer of the War Department (our map-maker), and I told him to put the Philippines on the map of the United States (pointing to a large map on the wall of his office), and there they are and there they will stay while I am President!

Many in retrospect have viewed this account of events with great cynicism and scorn, with the liberation of the Philippines from Spain supposedly having served as a premeditated excuse for its later annexation. However, some historians have recently argued that McKinley's "benevolent assimilation" of the Philippines was less a matter of premeditated avarice, and more of McKinley's sheer indecision/reluctance to have an initial coherent policy on the Philippines. In fact, many historians have encountered great difficulty in ascertaining the "baffling" and "enigmatic" decisions the President made, compounded by the fact that he was a very private person and rarely explained his reasonings to anyone else.

In his inaugural address in 1896, McKinley stated his first thoughts on imperialism: "We want no wars of conquest; we must avoid the temptation of territorial aggression." McKinley still favored a peaceful resolution to the tensions in Cuba with Spain, but popular sentiment drove him to war anyway - a war that was still largely a military success for the United States. Nevertheless, as the last president to have served in the civil war, it is still noting this quote of his at the onset of the sinking of the Maine: “I have been through one war; I have seen the dead piled up; I do not want to see another."

At the same time in 1898, Hawaii was also annexed on account of McKinley's supposed fears of a takeover by the Japanese or other powers. Guam and Puerto Rico were quick to be assimilated while Cuba was to become a temporary protectorate for a couple of years, but the Philippines was a different matter entirely for the American people due to several reasons:

• There was a reluctance to conquer large and densely populated areas, as shown by the previous colonial misadventures of Britain in India and France in her African holdings. Commodore George Dewey initially favored retaining only Manila and the naval base at Cavite for commercial and strategic purposes in the Pacific.
• Much like in Cuba, there was a burgeoning revolutionary movement in the Philippines by the natives. The struggles of the Cuban independence movement, however, were more familiar to Americans. Moreover, the Teller amendment to the US declaration of war on Spain barred the United States from annexing Cuba; it is unclear whether it should have also been applied to the Philippines.
• There were already some strong anti-imperialist leanings in the press, not necessarily out of concern for the welfare of the natives but for more xenophobic/less idealistic reasons, like the costs of "civilizing" the Philippines and the possibility of more foreigners voting in Congress, as well as certain economic interests fearing foreign competition.
• Unlike Hawaii, the Philippines was considered too far to serve as a "natural land barrier" to the American mainland. But much like in the Hawaiian debate, anti-imperialists also derisively spoke of future "Mongoloids" in the union.
• The two-party system was not cleanly split over the issue, and both Democrats and Republicans faced internal infighting on the choices of annexation, limited imperialism, or independence.

Amidst all this, however, McKinley receded from the public view, and most of what we can rely on are quotes from his acquaintances as well as some speculation. But in October 1898, seven months after Dewey's victory at Manila Bay earlier that April, McKinley made public in a series of announcements his intention to annex the entire Philippine archipelago as part of the deal with Spain in the Treaty of Paris. This could be attributed to several factors:

• Many politicians at the time perceived war to be generally popular among the American populace, and popular sentiment was something any president would have been keen on during the midterm elections in 1898. In preparation for his announcements, McKinley first went on a tour of the Midwest where crowds enthusiastically cheered his promises of annexation.
• Protestant sectors of the populace favored annexation (while most Catholics did not). McKinley was himself Protestant and would have looked favorably upon the "Christianization" of an already majority-Catholic Philippines.
• In an apparent reversal of opinion, American military men in Paris advised McKinley and his representatives that the occupation of anything short of the entire archipelago would be militarily indefensible. Some of these military men like Dewey also derided the capacities of the Filipino revolutionary leadership, who were themselves now growing disillusioned with the American blockade at Manila.

In December 1898, McKinley ordered General Elwell Otis to publicly disseminate his Benevolent Assimilation Proclamation, which commanded the population of the Philippines to respect the "supremacy" of American authority following the Treaty of Paris, which in return would also safeguard the private rights and property of the Filipinos. Otis recoiled at having to issue such a strongly worded declaration and made to replace some words like "supremacy", but an original copy leaked through to Aguinaldo who then hastily prepared for war. In February 1899, fighting broke out in the suburbs of Manila and would continue on from there. McKinley never lived to see what would ultimately become of his decision in the Philippines on account of his assassination in 1901.

Sources:

• In Our Image: America's Empire in the Philippines by Stanley Karnow
• The Philippine War, 1899-1902 by Brian McAllister Linn
• "Benevolent Assimilation": The American Conquest of the Philippines, 1899-1903 by Stuart C. Miller
• Ragtime in the White House: War, Race and the Presidency in the Time of William McKinley by Eliot Vestner