A party of Aguinaldo's men led by Agapito Bonzón and José Ignacio Paua met with Bonifacio at his camp in Indang. Unaware of the order for his arrest, Bonifacio received them cordially. The next day, Bonzón and Paua attacked Bonifacio's camp. Bonifacio did not fight back and ordered his men to hold their fire, though shots were nevertheless exchanged. In the crossfire, Bonifacio was shot in the arm, and Paua stabbed him in the neck and was prevented from striking further by one of Bonifacio's men, who offered to be killed instead. A brother, Ciriaco, was shot dead, while his other brother Procopio was beaten senseless, and his wife Gregoria may have been raped by Bonzón.^[66]
Bonifacio's party was brought to Naik, where he and Procopio stood trial on charges of sedition and treason against Aguinaldo's government and conspiracy to murder Aguinaldo.^[65][67] The jury was composed entirely of Aguinaldo's men and even Bonifacio's defence lawyer himself declared his client's guilt. Bonifacio was barred from confronting the state witness for the charge of conspiracy to murder on the grounds that the latter had been killed in battle, but after the trial the witness was seen alive with the prosecutors.^[68][69]
The Bonifacio brothers were found guilty despite insufficient evidence and recommended to be executed. Aguinaldo commuted the sentence to deportation on 8 May 1897, but Pío del Pilar and Mariano Noriél, both former supporters of Bonifacio, persuaded him to withdraw the order for the sake of preserving unity. In this they were seconded by Mamerto Natividád and other bona fide supporters of Aguinaldo.^[70] The Bonifacio brothers were executed on 10 May 1897 in the mountains of Maragondon.^[70][71] Apolinario Mabini wrote that Bonifacio's death demoralized many rebels from Manila, Laguna and Batangas who had come to help those in Cavite, and caused them to quit.^[39] In other areas, some of Bonifacio's associates like Emilio Jacinto never subjected their military commands to Aguinaldo's authority.^[