The Spanish authorities confirmed the existence of the Katipunan on 19 August 1896. Hundreds of Filipino suspects, both innocent and guilty, were arrested and imprisoned for treason. José Rizal was then on his way to Cuba to serve as a doctor in the Spanish colonial army in exchange for his release from Dapitan. When the news broke, Bonifacio first tried to convince Rizal, quarantined aboard a ship in Manila Bay, to escape and join the imminent revolt. Bonifacio, Emilio Jacinto and Guillermo Masangkay disguised themselves as sailors and went to the pier where Rizal's ship was anchored. Jacinto personally met with Rizal, who rejected their rescue offer. Rizal himself was later arrested, tried and executed
Some historians such as Milagros Guerrero, Emmanuel Encarnación, and Ramón Villegas have pushed for the recognition of Bonifacio as the first President of the Philippines instead of Aguinaldo, the officially recognised one. This view is based on his position of President/Supremo of the Katipunan revolutionary government from 1896–97. This view also emphasises that Bonifacio established a government through the Katipunan before a government headed by Aguinaldo was formed at the Tejeros Convention. Guerrero writes that Bonifacio had a concept of the Philippine nation called Haring Bayang Katagalugan("Sovereign Tagalog Nation") which was displaced by Aguinaldo's concept of Filipinas. In documents predating Tejeros and the First Philippine Republic, Bonifacio is called the president of the "Tagalog Republic"
José Rizal is generally considered the National hero, but Bonifacio has been suggested as a more worthy candidate on the grounds of having started the Philippine Revolution.Teodoro Agoncillo notes that the Philippine national hero, unlike those of other countries, is not "the leader of its liberation forces". Renato Constantino writes that Rizal is a "United States-sponsored hero" who was promoted as the greatest Filipino hero during theAmerican colonial period of the Philippines – after Aguinaldo lost the Philippine–American War. The United States promoted Rizal, who was taken to represent peaceful political advocacy, instead of more radical figures whose ideas could inspire resistance against American rule. Specifically, Rizal was selected over Bonifacio who was viewed as "too radical" and Apolinario Mabini who was "unregenerate."
Historian Ambeth Ocampo gives the opinion that arguing for Bonifacio as the "better" hero on the grounds that he, not Rizal, began the Philippine Revolution, is moot since Rizal inspired Bonifacio, the Katipunan and the Revolution. Even prior to Rizal's banishment to Dapitan, Rizal was already regarded by the Filipino people as a national hero, having been elected as honorary president by the Katipunan. Leon Ma. Guerrero notes that while Rizal did not give his blessing to Bonifacio because he believed the time was premature, he did not condemn the aim of independence per se. Teodoro Agoncillo gives the opinion that Bonifacio should not replace Rizal as national hero, but they should be honored "side by side"
Bonifacio's bones
In 1918, the American-sponsored government of the Philippines mounted a search for Bonifacio's remains in Maragondon. A group consisting of government officials, former rebels, and a man reputed to be Bonifacio's servant found bones which they claimed were Bonifacio's in a sugarcane field on 17 March. The bones were placed in an urn and put into the care of the National Library of the Philippines. They were housed at the Library's headquarters in the Legislative Building in Ermita, Manila, together with some of Bonifacio's papers and personal belongings. The authenticity of the bones was much disputed at the time and has been challenged as late as 2001 by Ambeth Ocampo. When Emilio Aguinaldo ran for President of the Commonwealth of the Philippines in 1935, his opponent Manuel L. Quezón (the eventual victor) invoked the memory of Bonifacio against him, the bones being the result of Bonifacio's execution at Aguinaldo's hands. During World War II, the Philippines was invaded by Japan in 1941. The bones were lost due to the widespread destruction and looting during the Allied capture of Manila in February 1945.