The film starts with Dr. Jose Rizal (Cesar Montano) in Ghent, Belgium, supposedly writing his second novel, El Filibusterismo. As the narration during the opening minutes continued, scenes that illustrate Rizal’s first novel, “Noli Me Tanger” was shown and Crisostomo Ibarra and his alter ego, Simoun, (Joel Torre) was introduced. This stood more as a second story of the movie as the said scenes progress throughout the movie as Rizal’s thoughts. As the two novels spread throughout the Philippines, a certain and somewhat unassuming character in the name of Andres Bonifacio grabs a hold of a copy of a Rizal novel and instigates a rebellion with his founded Katipunan which upheld a full-blown revolution. Archbishop Bernardo Nozaleda (Peque Gallaga) takes notice of this, claiming that Rizal gave the primary incentive in the revolution and warns Governor-general Blanco (Bon Vibar) that if he does not take care of Rizal and the growing conflict, he will be replaced. As the hunt for Rizal continues, the Spaniards get a hold of his older brother, Paciano Rizal (Pen Medina) and tortures him to get to Rizal. Paciano does not give any information on whether Rizal was the source of rebellion or not and was continued to be tortured, only to find out that he was already captured by the Spaniards later on. Paciano was eventually released and left their home together with his father,Francisco Mercado. Rizal is then seen being escorted by the Spanish guards to be interrogated by a colonel who is convinced that Rizal is a traitor since his latest novel was dedicated to Father Gomez, Burgos and Zamora.
Father Gomez, Father Burgos and Father Zamora were then seen being executed by garrote for treason. This was witnessed by the young Paciano (Ping Medina), who was also a close friend of the three priests. This ultimately raised Paciano’s political awareness as he influences his 11 year-old brother. Rizal was then enrolled in a local school wherein he had a hard time as he was disliked