Before 1872, numerous uncoordinated revolts against Spanish colonialism, like those led by Gabriela Silang, Palaris, and Tamblot, were easily suppressed. Early religious revolts in the 17th century, including Bancao, Sumuroy, and Tapar, aimed to restore indigenous religions. Hermano Pule continued this tradition; his Cofradia de San Jose was brutally crushed in 1841, leading to his dismemberment. This suppression sparked the Tayabas regiment's revolt in 1843, who, inspired by Hermano Pule, attacked Fort Santiago shouting for independence, though they ultimately failed. Hermano Pule's dealings with Father Pedro Pelaez, a pioneer of the secularization movement, link the fight for religious freedom to the Gomburza, signifying a continuous, albeit evolving, struggle for self-empowerment and independence.

The Glorious Revolution in Spain in 1868 brought a liberal government and Governor-General Carlos Maria de la Torre to the Philippines, implementing progressive changes from 1869 to 1871. However, the subsequent restoration of the monarchy led to the arrival of the strict Governor-General Rafael de Izquierdo, who reversed these liberal policies. The 19th century also saw significant economic shifts, such as the abolition of the Galleon Trade and the opening of the Philippines to world trade in 1834. The 1869 opening of the Suez Canal facilitated faster travel and the influx of liberal European ideas from thinkers like Voltaire, Rousseau, and Locke, and the ideals of the French and American Revolutions. These ideas, emphasizing rights and equality, fueled a growing progressive sentiment among Filipinos, creating an atmosphere of discontent towards the slow pace of reform.

The respect once held for indigenous babaylans transferred to the friars, who accumulated immense power due to their long tenures in parishes, in contrast to the short terms of civil officials. This 'monastic supremacy,' as Marcelo H. del Pilar termed it, led to abuses of power, including land grabbing and derogatory views of Filipinos as 'Indios.' Policies like polo y servicios and the encomienda system further exploited the populace. Friars also gained significant financial and political power through haciendas. The widespread displacement of people, particularly in Cavite, led to an increase in 'banditos' who sought justice, earning Cavite the moniker 'La Madre de los Ladrones.' The uprisings in Silang in 1745 exemplify the persistent agrarian unrest that continued into the 19th century.

Father Mariano Gomes, originally from Sta. Cruz, Manila, served as the beloved parish priest of Bacoor, Cavite, for 48 years. He was known for his community work, building roads, improving services, and fostering economic development, even mediating agrarian disputes like the Luis Parang case. Father Jacinto Zamora, from Pandacan, Manila, was academically brilliant, achieving top ranks in priestly appointments alongside Burgos. He served in several parishes, including Batangas, Pasig, and Marikina. Father Jose Burgos, a Criollo born in Vigan, Ilocos, was the most famous, holding seven degrees (two doctorates) by age 35. He was a respected teacher and close to high church officials, a known liberal, and friend of Governor-General Carlos Maria de La Torre. While Gomes was the oldest and Zamora and Burgos were younger, all three received extensive education at institutions like Letran and UST, and were vital figures in the movement for secularization.

The 1850s and 1860s saw a resurgence of the secularization movement, spearheaded by Father Pedro Pelaez (and later Jose Burgos). This movement demanded that parishes, traditionally managed by secular priests, be returned from the friars (regular priests). The Council of Trent had initially stipulated that regular priests (friars) should focus on mission work, while secular priests handled parishes. However, due to a shortage of Spanish secular priests, regulars took over parishes, gaining significant power and privileges. The expulsion of the Jesuits in 1768 temporarily empowered secular priests, but their return in 1859 led to a domino effect where seculars lost their parishes, intensifying calls for secularization. This struggle was deeply rooted in racial discrimination, as Spanish friars viewed Filipino priests as inferior and suspected them of plotting revolts, a fear amplified by the example of Mexico’s independence movement led by Father Miguel Hidalgo.

Father Pedro Pelaez, a mentor to Burgos, was a central figure in the secularization movement but tragically died in the 1863 earthquake. The struggle was continued by the "Committee of Reformers," which included Fathers Gomes, Zamora, and Burgos, alongside progressive businessmen, lawyers, and journalists. This committee advocated for reforms to advance the Philippines. Their ideas resonated with students from the University of Santo Tomas (UST). In the 'demonstration of 1869,' these students distributed leaflets asserting that 'indios' deserved respect and should not be denigrated by their professors, a direct challenge to Spanish racial prejudice. These students, including future national figures like Maximo Paterno and Paciano Rizal, formed one of the first student movements in the Philippines, fueled by a desire for dignity and honor despite their economic prosperity.

The Cavite Mutiny erupted on January 20, 1872, initially appearing as a localized revolt of disgruntled Filipino soldiers at the Fort San Felipe arsenal in Cavite City led by Sgt. La Madrid, who were stripped of privileges by Governor-General Izquierdo. However, historian Fr. John Schumacher argued for a larger conspiracy involving Filipino liberals aiming to overthrow the government. A letter revealing this plot to Governor-General Izquierdo led to the pre-emptive discovery of a planned mutiny in Manila, sparing the capital from an uprising. Maximo Inocencio, Crisanto de los Reyes, and Enrique Paraiso, masons, were identified as masterminds and exiled. The blame, however, was conveniently shifted to the three priests, Gomes, Burgos, and Zamora, who were implicated by a false testimony from Francisco Zaldua, a mutineer who later recanted.

The three priests, Fathers Mariano Gomes, Jacinto Zamora, and Jose Burgos, were arrested and subjected to a swift military trial. Despite a lack of direct evidence, they were convicted as the brains behind the mutiny, a verdict questioned by many, including Archbishop Meliton Martinez, who refused Izquierdo's order to defrock them and chose to toll the bells, signifying his belief in their innocence. On February 17, 1872, they were executed by garrote in Bagumbayan (now Luneta). Zaldua was executed first, followed by Gomes, who faced death calmly. Zamora, already mentally disturbed, was quiet and stunned, while Burgos, distraught, cried out his innocence. Their bodies were secretly buried, later believed to be in Paco Cemetery. Many found their execution, especially of priests, deeply shocking and unjust.

The martyrdom of GOMBURZA had a profound impact on Filipino nationalism. Emilio Jacinto’s essay and the Katipunan's use of 'Gomburza' as a password underscored their rallying cry for revenge against Spanish injustices. Historian Teodoro Agoncillo argued that 1872 marked the beginning of true Filipino national consciousness, transforming regional identities into a unified Filipino identity. Jose Rizal, influenced by his brother Paciano, dedicated his novel 'El Filibusterismo' to the three priests, solidifying their place in the national narrative. Their execution was a catalyst for the Propaganda Movement, which sought reforms, and subsequently, for Bonifacio's Katipunan and the broader Philippine Revolution, as it united Filipinos against colonial oppression and ignited the fight for independence.