Decline and fall of the First Philippine Republic :-

The Philippine Army continued suffering defeats from the better armed American Army during the conventional warfare phase, forcing Aguinaldo to continuously change his base of operations, which he did off and on for nearly the length of the entire war.

On March 23, 1901, General Frederick Funston and his troops captured Aguinaldo in Palanan, Isabela with the help of some Filipinos (called the Macabebe Scouts after their home locale) who had joined the Americans' side. The Americans pretended to be captives of the Macabebes, who were dressed in Philippine Army uniforms. Once Funston and his “captors” entered Aguinaldo's camp, they immediately fell upon the guards and quickly overwhelmed them and the weary Aguinaldo.

On April 1, 1901, at the Malacañang Palace in Manila, Aguinaldo swore an oath accepting the authority of the United States over the Philippines and pledging his allegiance to the American government. Three weeks later he publicly called on his followers to lay down arms. “Let the stream of blood cease to flow; let there be an end to tears and desolation,” Aguinaldo said. “The lesson which the war holds out and the significance of which I realized only recently, leads me to the firm conviction that the complete termination of hostilities and a lasting peace are not only desirable but also absolutely essential for the well-being of the Philippines.”

The capture of Aguinaldo dealt a severe blow to the Filipino cause, but not as much as the Americans had hoped. The less competent General Mariano Trias succeeded him, but surrendered shortly after.

Command then fell to the highly regarded General Miguel Malvar, who originally had taken a defensive stance against the Americans, but now launched all-out offensives against the American-held towns in the Batangas region. Though his victories were small, they were a testament that the war was not yet over.

In response, General J. Franklin Bell performed tactics that countered Malvar's guerilla strategy perfectly. Forcing civilians to live in hamlets, interrogating suspected guerillas (and regular civilian alike), and his execution of scorched earth campaigns took a heavy toll on the Filipino revolutionaries.

Bell also relentlessly pursued Malvar and his men, breaking ranks, dropping morale, and forcing the surrender of many of the Filipino soldiers. Finally, in April of 1902, after barely escaping capture, Malvar with his sick wife and children along with some of his most trusted officers who stood with him until the end, surrendered. By the end of the month, nearly 3,000 of Malvar's men also gave into the inevitable and surrendered.

With the surrender of Malvar, the last truly capable general of the Philippine Army, the Filipino fight began to dwindle even further. Command changed hands frequently, as each general, one after another, was killed, captured, or just surrendered.
The United States government declared the “insurgency” officially over in 1902. The Filipino leaders for the most part, accepted that the Americans had won.

However, some Filipino nationalist historians consider the war to have continued for nearly a decade, since bands of guerillas, quasi-religious armed groups and other resistance groups continued to roam the countryside, still clashing with American Army or Philippine Constabulary patrols. These groups, which included Macario Sakay, a senior Katipunan member and general who attempted to form a new Tagalog Republic, and the pulajanes, colorum or Dios-Dios groups of assorted provinces, were dismissed as bandits, fanatics or cattle rustlers. Sakay was captured and executed in 1907, while the last of the latter groups were wiped out or had surrendered by 1913.