In his paper External Discipline during Conterinsurgency: A Philippine War Case Study, 1900—1901., John S. Reed asserts that military operations during the Philippine-American War moved through three distinct phases

1. Between February and December 1899, the U.S. Eighth Army Corps defeated the Philippine Republic's conventional field army in Central Luzon.
2. In the war's second phase, between January 1900 and May 1901, U.S. troops forced most guerrilla bands throughout the archipelago to surrender under the dual pressure of local offensive patrols, or "hikes," and martial law coercion exerted through provost courts and military commissions.
3. The war's third and final phase took place in South-central Luzon and the Visayan island of Samar, subdued between September 1901 and April 1902, or shortly after the introduction of population reconcentration and widespread property destruction outside designated secure zones.

Two distinct points can be gleaned from Reed's categorization. First, the Philippine war was predominantly a guerilla conflict more than a conventional war. In the 41-month conflict since its start in February 1899 and conclusion in July 1902, guerilla warfare was waged for over 30 months, or 73 percent of the period. Second, Reed acknowledges how the conduct of war in Batangas and Samar during the final phase of the campaign escalated into punitive actions and harsh measures (reconcentration).

With the capture of Gen. Emilio Aguinaldo by Gen. Funston's troops in March 1901, General Miguel Malvar took over and assumed the overall responsibilities until his surrender in April 1902. Malvar was supreme commander for over 13 months. Aguinaldo was at the helm for 66 percent of the period while Malvar was in charge for one-third of the duration. As head of the Philippine resistance, the Americans pursued Malvar with the same vigor as they did Aguinaldo.

The Philippine-American war as it manifested in Batangas province can be broken down into several stages:
(Battle for Batangas, A Philippine province at war., Glenn Anthony May)

1. the early operations of the Americans south of Manila in the second half of 1899;
2. the invasion and occupation phase of Batangas, characterized by the initial blitzkrieg by the forces of Lloyd Wheaton, succeeding mopping up operations, the establishment of garrisons in key towns and hikes, and patrols into the bush from January 1900 to March 1901;
3. the resurgence and rejuvenation of the Batangas guerilla movement due to the efforts of Malvar after the capture of Aguinaldo, from April 1901 until December 1901;
4. the reconcentration and conquest period with Gen. Bell's assumption of command of the US Army Third Brigade beginning December 1901;

A total of five American commanders were appointed to address Malvar's "insurgency". As commanders of the Batangas theater operations, Gen. Lloyd Wheaton, Lt Col. William Birkhimer, Gen. Robert Hall, Gen. Samuel Sumner all preceded Gen. Franklin Bell, who eventually brought about Malvar's surrender.