The organization almost broke up when on July 4, 1942, when the Japanese raided its headquarters and killed its commander, Miguel Ver. What followed was a continuous evasion enemy from punitive expeditions and of continued efforts to survive by contacting and affiliating with other guerrilla units.

In November 1943, Eleuterio Adevoso, a PMA cadet Class 1944, succeeded in reorganizing the Hunters, with the assistance of Augusto Gonzales (advisor), Tereso Pia (Chief of Staff, ROTC - Jose Rizal College), Pacifico Jose (G1, PMA - Class of 1944), Frisco San Juan (G2, PMA - Class of 1944), and Inocencio Fabia (G4). Designated as field commanders were Amado Bagalay, Juanito Ferrer, Justiniano Estrella, Emmanuel de Ocampo, Vicente Estacio, Catalino Estrella, and Catalino Nera. The guerrilla force soon grew into a large unit whose area of operations covered not only Manila but also Bulacan and Cavite.Throughout the remaining period immediately preceding the liberation campaign around Manila, the Hunters busied themselves with guerrilla operations. They established a productive intelligence network inside Manila, and performed harrassment operations against Japanese units in the city.

The Hunters were not immune to the intense rivalry that marked Inter-Guerrilla group relations, and throughout the period affiliated themselves with a number of other guerrilla groups, after they became at odds with Marking's Guerrillas.