Bonifacio refused to recognize Aguinaldo’s government. He thought he was still
    the Supremo of the Katipunan government. In fact, he formed a new government wholly
    separate and independent from the one formed at the Tejeros convention. The following
    month he drafted a military agreement in Naic, Cavite. It was signed by about forty men.
 

Bonifacio and his men left Naic for barrio Limbon in the nearby town      of Indang. On April 26, 1897, Bonifacio was arrested by two loyal      officers of Aguinaldo – Colonel Agapito Bonzon and Aguinaldo’s      brother-in-law Major Jose Ignacio Paua. Bonifacio and his men      put up a fight. Andres’s brother Ciriaco was killed. The Supremo      himself was shot in his left arm. Major Paua jumped at Bonifacio      and stabbed the left side of his neck with a dagger. From Indang,      a half-starved and wounded Bonifacio was carried by hammock      to Naic,  which had become President Aguinaldo’s headquarters.          Andres Bonifacio was tried by the military court in Maragondon,      Cavite. He was charged with treason and trying to overthrow the new     president and his government. One witness even swore that he was

Col. Agapito Bonzon

     paid ten pesos by Bonifacio to kill Aguinaldo. By some accounts Andres was not given a fair
     chance to defend himself.
 
        On May 8, 1897, Andres and Procopio Bonifacio were sentenced to death. However,
    according to Aguinaldo, he changed their sentence and asked for them to be exiled instead.
    But Aguinaldo was advised by his generals to go ahead with the death sentence. They reasoned
    that Bonifacio’s death was necessary to protect the best interests of the revolution. Alive,
    Bonifacio would only threaten and divide the revolutionary forces.