(Rizal was not directly a part of the Katipunan, even denouncing the group and disagreeing with the cause. However, he served as an inspiration to its members and was considered as its honorary president, with his name even serving as a password for the higher ranking members of the movement.)
Rizal's arrest and his exile in 1892 bestirred a chain of events that lead directly to armed insurrection for national independence. On the night of Rizal's arrest, Andres Bonifacio, a self-educated man of humble origins, founded a secret society, the Katipunan (The Highest and Most Respectable Association of the Sons of the People), modeled on the Masonic Order and committed to winning independence from Spain through revolution.
The Katipunan, like the Masonic lodges, had secret passwords and ceremonies, and its members were organized into ranks or degrees, each having different colored hoods, special passwords, and secret formulas. New members went through a rigorous initiation, which concluded with the pacto de Sangre, or blood compact.
From its origins in the Tondo district of Manila, the Katipunan spread gradually to the provinces and by August 1896 – on the eve of the revolt against Spain – it had about 30,000 members, both men and women. Most of them were members of the lower-and lower-middle-income strata, including peasants. The nationalist movement had effectively moved from the closed circle of prosperous ilustrados to a truly popular base of support.
The organization grew very rapidly because the insolent and provocative way in which the friars carried out their campaign against reforms had annoyed the masses. It perhaps too grew so well, because the organization of political associations was prohibitted on the archipelago and thus the middle class, which was the most educated and influential, not being able to move freely, could not support openly die Liga Filipina, since that class was more in favour of the Liga's program, even after having endured most cruel sufferings.
On June 21, 1896. Dr. Pio Valenzuela, Bonifacio's emissary, visited Rizal in Dapitan and informed him of the plan of the Katipunan to launch a revolution. Rizal objected to Bonifacio's bold project stating that such would be a veritable suicide. Rizal stressed that the Katipunan leaders should do everything possible to prevent premature flow of native blood. Valenzuela, however, warned Rizal that the Revolution will inevitably break out if the Katipunan would be discovered.
Sensing that the revolutionary leaders were dead set on launching their audacious project, Rizal instructed Valenzuela that it would be for the best interests of the Katipunan to get first the support of the rich and influential people of Manila to strengthen their cause. He further suggested that Antonio Luna with his knowledge of military science and tactics, be made to direct the military operations of the Revolution.
In another Spanish colony, 15,000 km away, the Cuban revolution for independence started in February 1895. To escape from his exile, Rizal volunteered to serve as a doctor for the Spanish army in Cuba. Rizal's offer was accepted but just as he left for Cuba by ship, the Spanish learned of the existence of the revolutionary society Katipunan because of the untimely discovery by a Spanish friar, on August 19th, 1896. The Spanish began making hundreds of arrests and Bonifacio had little choice but to issue the call to arms, the Cry of Balintawak, on August 26th, 1896.
Bonifacio and Emilio Jacinto attacked the Spanish garrison at San Juan on August 29th, 1896 with 800 Katipuneros. Insurrections also broke out in eight provinces surrounding Manila on Luzon and soon spread to other islands. The rebels we not trained regulars and had little success against the colonial troops. In the province of Cavite, however, under the leadership of Emilio Aguinaldo, the Katipunan rebels defeated the Civil Guard and the colonial troops.
Meanwhile, Rizal was arrested in transit to Cuba and ordered to return to Fort Santiago in Manila to stand trial for rebellion, sedition and illicit association. On December 22nd, 1896, Rizal, held incomunicado in Fort Santiago, wrote a "manifesto" to his countrymen to stop fighting, condemning the absurd revolution. The Spanish authorities did not publish this "manifesto". He was tried on December 26th, found guilty and condemned to death. Jose Rizal was shot by a firing squad on December 30th, 1896. Rizal's execution gave the rebellion fresh determination.
Andres Bonifacio led the Revolution in its early stages, although he did not excel in the field of battle like Emilio Aguinaldo, who distinguished himself in the battlefields in Cavite, at that time the heartland of the Revolution. Due to his successes in battle, Aguinaldo was elected to replace Bonifacio. Bonifacio withdrew his supporters and the two factions began to fight. Bonifacio was arrested, tried and executed on May 10th, 1897 by Aguinaldo's order.
Aguinaldo's forces were driven from Cavite to Bulacan where Aguinaldo declared the constitution and established the Republic of Biak-na-Bato. Both sides soon came to realize that the struggle between Spain and the new Republic had reached an impasse. Both, Filipino and Spanish forces, were unable to pursue hostilities to a successful conclusion.
Consequently, Negotiations began in August and concluded in between November 18th and December 15th with the Pact (truce) of Biak-na-Bato. The agreement extended a general amnesty to the rebels with a payment of US$800,000 for Aguinaldo and his government to retire in voluntary exile to Hong Kong. Aguinaldo left the Philippines with his government on December 27th, 1897. While in Hong Kong, Aguinaldo and his compatriots designed what is today the Philippine national flag.