Faced with the potential threat from within, General Aguinaldo, upon learning of the steps taken by the regional government of Batangas in recognizing Bonifacio's authority, immediately issued a circular reminding the Batangueños of their responsibility to the revolutionary government. He instructed the Batangueño chiefs "to perfect the organization of our army" because it was solely upon its efficiency that the attainment of the country's welfare depended.

The document (letter) showed what Aguinaldo felt in the face of the serious situation and the precise steps that he would follow in dealing with those who would act contrary to the established principles of the revolutionary government. His complete knowledge of Bonifacio's intentions, particularly the seditious Acta de Tejeros, the Naik Military Agreement, and the appointment of Emilio Jacinto, on April 15, 1897, as commander-in-chief of the North Military Area, comprising Manila and the outlying provinces--acts that exhibited abundant proofs of Bonifacio's repudiation of the revolutionary government and his assumption of supreme powers--prompted Aguinaldo to order the arrest of Bonifacio, who, by this time, had already transferred to the barrio of Limbon, Indang, in preparation for his departure from Cavite.

Aguinaldo's order for Bonifacio's arrest was the result of the numerous complaints that the former had received from some leaders who had reason to suspect the Supremo of some acts that were probably not true but nonetheless believed in by the majority. It is interesting to note that though the target of Bonifacio's wrath was the Magdalo faction, yet the charges filed against him were those penned by the Magdiwang man, Severino de las Alas.