Following the end of the war in 1902, Isabelo de los Reyes was working towards the formation of a national church, that is independent of Rome. On 3 August he suggested that Aglipay be its first bishop. Aglipay, a Catholic at the time, was reluctant, but accepted de los Reyes' offer to establish an independent church. On 18 January 1903, Aglipay was appointed Supreme Bishop of the "Philippine Independent Church". As Supreme Bishop he allied himself with the nationalist and most radical political parties during his time like the Sakdalistas and later on even with the Socialist and Communist Parties.