The goal, or end-state, sought by the Filipino insurgency was a sovereign, independent, socially stable Philippines led by the illustrado oligarchy. Local chieftains, landowners, and businessmen were the principales who controlled local politics. The insurgency was strongest when illustrados, principales, and peasants were unified in opposition to annexation. The peasants, who provided the bulk of guerilla manpower, had interests different from their illustrado leaders and the principales of their villages. Coupled with the ethnic and geographic fragmentation, unity was a daunting task. The challenge for Aguinaldo and his generals was to sustain unified Filipino public opposition; this was the revolutionaries strategic center of gravity.

The Filipino operational center of gravity was the ability to sustain its force of 100,000 irregulars in the field. The Filipino General Francisco Macabulos described the insurrection's aim as, “not to vanquish the US Army but to inflict on them constant losses.” They sought to initially use conventional (later guerilla) tactics and an increasing toll of US casualties to contribute to a negotiated peace. Their hope was that as more blood was spilled the US people elect the avowedly anti-imperialist William Jennings Bryan as President, and hopping he would withdraw from the Philippines. They pursued this long-term goal with guerilla tactics suited to this protracted struggle. In the long run their tactics were succesful but Aguinaldo died from a sudden attack of Malaria in 1908, too late to see his dream achived.

As of 1900, Aguinaldo ordered his army to engage in guerrilla warfare, a means of operation which better suited them and made American occupation of the Philippine archipelago all the more difficult over the next few years. In fact, during just the first four months of the guerrilla war, the Americans lost nearly 500 men who were either killed or wounded. The Filipino resistance fighters began staging bloody ambushes and raids. At first, it even seemed as if the Filipinos would fight the Americans to a stalemate and force them to withdraw. This was even considered by President McKinley at the beginning of the phase.

The shift to guerrilla warfare, however, only angered the Americans into acting more ruthlessly than before. They began taking no prisoners, burning whole villages, and routinely shooting surrendering Filipinos. Much worse were the concentration camps that civilians were forced into, after being suspected of being guerrilla sympathizers. Thousands of civilians died in these camps. In nearly all cases, the civilians suffered much worse than the actual Filipino guerrillas.

The subsequent American repression towards the population tremendously reduced the materials, men, and morale of many Filipino resistance fighters, compelling them in one way or another to surrender. Still that same terror made more Filipinos flock into the guerilla forces and the cycle of violence continued until the end of the war, especially outside of Luzon where General J. Franklin Bell was on command.