Thirteen years after leaving the Philippines, Crisostomo Ibarra returns as Simoun, a rich jeweler sporting a beard and blue-tinted glasses, and a confidant of the Captain-General. He cynically sides with the upper classes, encouraging them to commit abuses against the masses to encourage the latter to revolt against the oppressive Spanish colonial regime. His two reasons for instigating a revolution are at first, to rescue María Clara from the convent and second, to get rid of ills and evils of Philippine society. His true identity is discovered by a now grown-up Basilio while visiting the grave of his mother, Sisa, as Simoun was digging near the grave site for his buried treasures. Simoun spares Basilio’s life and asks him to join in his planned revolution against the government, egging him on by bringing up the tragic misfortunes of the latter’s family. Basilio declines the offer as he still hopes that the country’s condition will improve. Basilio, at this point, is a graduating medical student at the Ateneo Municipal. After the death of his mother, Sisa, and the disappearance of his younger brother, Crispín, Basilio heeded the advice of the dying boatman, Elías, and traveled to Manila to study.
Basilio was adopted by Captain Tiago after María Clara entered the convent. Simoun, for his part, keeps in close contact with the bandit group of Kabesang Tales, a former cabeza de barangay who suffered misfortunes at the hands of the friars. He was forced to give everything he had owned to the greedy, unscrupulous Spanish friars and the Church. Before joining the bandits, Tales took Simoun’s revolver while Simoun was staying at his house for the night. As payment, Tales leaves a locket that once belonged to María Clara. To further strengthen the revolution, Simoun has Quiroga, a Chinese man hoping to be appointed consul to the Philippines, smuggle weapons into the country using Quiroga’s bazaar as a front. Simoun wishes to attack during a stage play with all of his enemies in attendance. He, however, abruptly aborts the attack when he learns from Basilio that María Clara had died earlier that day in the convent. A few days after the mock celebration by the students, the people are agitated when disturbing posters are found displayed around the city.
The authorities accuse the students present at the pancitería of agitation and disturbing peace and has them arrested. Basilio, although not present at the mock celebration, is also arrested. Captain Tiago dies after learning of the incident. But before he dies he signs a will. His will originally states that Basilio should inherit all his property but due to this forgery his property is given in parts, one to Santa Clara, one for the archbishop, one for the Pope, and one for the religious orders leaving nothing for Basilio to be inherited. Basilio is left in prison as the other students are released. Basilio is soon released with the help of Simoun. Basilio, now a changed man, and after hearing about Julî’s suicide, finally joins Simoun’s revolution. Simoun then tells Basilio his plan at the wedding of Paulita Gómez and Juanito, Basilio’s hunch-backed classmate. His plan was to conceal an explosive which contains nitroglycerin inside a pomegranate-styled Kerosene lamp that Simoun will give to the newlyweds as a gift during the wedding reception. According to Simoun, the lamp will stay lighted for only 20 minutes before it flickers; if someone attempts to turn the wick, it will explode and kill everyone—important members of civil society and the Church hierarchy—inside the house.
Basilio has a change of heart and attempts to warn Isagani, his friend and the former boyfriend of Paulita. Simoun leaves the reception early as planned and leaves a note behind: Initially thinking that it was simply a bad joke, Father Salví recognizes the handwriting and confirms that it was indeed Ibarra’s. As people begin to panic, the lamp flickers. Father Irene tries to turn the wick up when Isagani, due to his undying love for Paulita, bursts in the room and throws the lamp into the river, sabotaging Simoun’s plans. He escapes by diving into the river as guards chase after him. He later regrets his impulsive action because he had contradicted his own belief that he loved his nation more than Paulita and that the explosion and revolution could have fulfilled his ideals for Filipino society. Simoun, now unmasked as the perpetrator of the attempted arson and failed revolution, becomes a fugitive.
Wounded and exhausted after he was shot by the pursuing Guardia Civil, he seeks shelter at the home of Father Florentino, Isagani’s uncle, and comes under the care of doctor Tiburcio de Espadaña, Doña Victorina’s husband, who was also hiding at the house. Simoun takes poison in order for him not to be captured alive. Before he dies, he reveals his real identity to Florentino while they exchange thoughts about the failure of his revolution and why God forsook him, when all he wanted was to avenge the people important to him that were wronged, such as Elias, Maria Clara and his father, Don Rafael. Florentino opines that God did not forsake him and that his plans were not for the greater good but for personal gain. Simoun, finally accepting Florentino’s explanation, squeezes his hand and dies. Florentino then takes Simoun’s remaining jewels and throws them into the Pacific Ocean with the corals hoping that they would not be used by the greedy, and that when the time came that it would be used for the greater good.