After thirteen years of being away from the Philippines, Crisóstomo Ibarra returns under the guise as Simoun, a rich jeweler sporting a beard and blue-tinted glasses, and a confidant of the Captain-General. Abandoning his idealism, he becomes a cynical saboteur, the titular filibustero, seeking revenge against the system responsible for his misfortunes by plotting a revolution. Simoun insinuates himself into Manila high society and influences every decision of the Captain-General to mismanage the country’s affairs so that a revolution will break out. He cynically sides with the upper classes, encouraging them to commit abuses against the masses so that the latter would be encouraged to revolt against the oppressive Spanish colonial regime. This time, he does not attempt to fight the authorities through legal means, but through violent revolution using the masses. Simoun has reasons for instigating a revolution. First is 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 student of medicine at the Ateneo Municipal de Manila. 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. With Captain Tiago’s help, Basilio was able to go to Colegio de San Juan de Letrán where, at first, he is frowned upon by his peers and teachers not only because of the color of his skin but also because of his shabby appearance which he also experience at Ateneo. Captain Tiago’s confessor, Father Irene is making Captain Tiago’s health worse by giving him opium even as Basilio tries hard to prevent Captain Tiago from smoking it. He and other students want to establish a Spanish language academy so that they can learn to speak and write Spanish despite the opposition from the Dominican friars of the Universidad de Santo Tomás. With the help of a reluctant Father Irene as their mediator and Don Custodio’s decision, the academy is established; however they will only serve as caretakers of the school not as the teachers. Dejected and defeated, they hold a mock celebration at a pancitería while a spy for the friars witnesses the proceedings.
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. Once a farmer owning a prosperous sugarcane plantation and a cabeza de barangay (barangay head), he was forced to give everything to the greedy and unscrupulous Spanish friars. His son, Tano, who became a civil guard was captured by bandits; his daughter Julî had to work as a maid to get enough ransom money for his freedom; and his father, Tandang Selo, suffered a stroke and became mute. 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 and as stated in his will—forged by Father Irene, all his possessions are given to the Church, leaving nothing for Basilio. Basilio is left in prison as the other students are released. A high official tries to intervene for the release of Basilio but the Captain-General, bearing grudges against the high official, coerces him to tender his resignation. Julî, Basilio’s girlfriend and the daughter of Kabesang Tales, tries to ask Father Camorra’s help upon the advice of an elder woman. Instead of helping Julî, however, Father Camorra tries to rape her as he has long-hidden desires for Julî. Julî, rather than submit to the will of the friar, jumps over the balcony to her death.
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 inside a pomegranate-styled lamp that Simoun will give to the newlyweds as a gift during the wedding reception. The reception will take place at the former home of the late Captain Tiago, which was now filled with explosives planted by Simoun. 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 the people inside, including Isagani, his friend and the former boyfriend of Paulita. Simoun leaves the reception early as planned and leaves a note behind;
"Mene Thecel Phares."
Juan Crisostomo Ibarra.
Initially thinking that it was simply a bad joke by those left behind, 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 soldiers, he seeks shelter at the home of Father Florentino, Isagani’s uncle, and comes under the care of Doctor Tiburcio de Espadaña, the husband of Doña Victorina, who was also hiding at the house. Simoun takes poison in order for him not to be captured alive by the authorities. Before he dies, he reveals his real identity to Father Florentino while they exchange thoughts about the failure of his revolution and why God forsook him. Father 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 Father Florentino’s explanation, squeezes his hand and dies. Father Florentino then takes Simoun’s remaining jewels and throws them into the sea, 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, when the nation would be finally deserving liberty for themselves, the sea would reveal the treasures.
