In 1938, when the PSP merged with the Partido Komunista ng Pilipinas, Alejandrino held a position in the party's central committee.
During the 1940 elections, Alejandrino ran under the AMT-endorsed Popular Front ticket and won a seat as mayor of Arayat.
[2]: 82 During World War II, members of the PKP along with peasant groups such as the AMT and the Kalipunang Pambansa ng Magbubukid sa Pilipinas (KPMP) convened in Cabiao, Nueva Ecija, to discuss organization, strategy, and tactics.
A Central Luzon Bureau was formed and Alejandrino was elected as second-in-command of its military committee, under Luis Taruc.
A month later, on March 29, 1942, peasant guerrillas and members of the AMT and the KPMP met again in Cabiao to form the Hukbalahap.
[3]: 30–31 During this time, Alejandrino adopted multiple aliases, such as Guan Yek (GY), Torres, GI, and Tatang.
[4] Alejandrino participated in guerrilla activity at this time, commanding Reco 3 in addition to his duties as General HQ vice-commander.
This lack of recognition, combined with peasant abuses by the landowning class, and the results of the 1946 elections, added to the growing unrest in Central Luzon.
As a result of this, the peasantry took to arms against the government in open rebellion, reforming the Hukbalahap as the Hukbong Mapagpalaya ng Bayan (HMB).
In 1957, Alejandrino met up with remnants of the HMB in Zambales and gradually implemented a strategy of legal struggle, ending the armed rebellion of the Hukbalahap.