El Filibusterismo starts with the sailing of the ship Tabo from Manila to Laguna. One of the passengers was Simoun, a jeweller who was actually Juan Crisostomo Ibarra in disguise. Also on the ship were Isagani and Basilio. This novel narrates the events 13 years after the death of Elias and Sisa.
Basilio went to San Diego and while visiting the burial ground of his mother Sisa, met Simoun. He saw through Simoun's disguise; and to make sure his secret remains such, Simoun attempted to finish Basilio off. After a failed attempt at Basilio's life, Simoun then encourages Basilio to take part in his plan to overthrow the Spanish Government in the Philippines. In the interest of his studies, Basilio refused.
While the Captain General was entertaining himself in Los Baņos, a group of Filipino students were preparing a request for the institution of an academy of the Spanish language, to be forwarded to the King of Spain. This request was not granted, because the latter found out that the request would not be fulfilled according to the specifications of the students, but instead will be managed by the friars, putting the students on the passive end of the deal. Therefore, they would not have any say on the management of the academy.
Meanwhile, Simoun met with Basilio and once again encouraged the latter to side with him in his plans to rage an uproar, and sneak Maria Clara out of the convent in which she lives as a nun. But this plan was not put into reality because Maria Clara died that afternoon.
The students, on the other hand, in order to overcome their frustration for not being able to establish an academy, went to a restaurant and had a small gathering. While eating, some of the students delivered speeches that directly attacked the misdeeds of the friars. This incident reached the knowledge of the friars and so the next day papers were found stuck to the doors of the university in which were written threats, and other such grave writings. This act was blamed on the students and they were consequently arrested. Basilio was included in this group of students, which caused his girlfriend Juli much grief.
Because relatives of these students mediated for them, they were freed. Basilio, on the other hand, had no one to mediate for him because Capitan Tiyago, who took him in when he was studying, had already died; his mother was also dead. Juli asked Pari Camorra to help her get Basilio out but instead of helping her, he caused her death.
Meanwhile, for Simoun to get his revenge, he hooked up with Timoteo Pelaez, father of Juanito Pelaez. He was able to arrange a wedding between Juanito and Paulita Gomez. He invited influential people to attend the wedding, and even got the Captain General to be one of the godfathers of the couple.
After two months of being in jail, Basilio was finally freed with the help of Simoun. He immediately went to Simoun to offer his help in the fulfillment of latter's plans. Simoun took this as an opportunity to show the youngster the bomb he has created, which was as big as a human head. This was in the form of a lamp which he will present to the couple as his gift. He will then request that the lamp be hung in the middle of the house in which the reception will take place. After 20 minutes the lamp's brilliance will fade. When the wick is raised in an attempt to re-light the lamp, a fulminato de mercurio capsule will go off. The bomb will explode, and with it goes the house and the people therein. The huge blast of the bomb will signal the start of Simoun's uproar.
Barely 7 in the evening of the wedding day, Basilio paced in front of the house where the feast will be held. Simoun left the house to avoid the upcoming explosion; Basilio turned to follow Simoun but Isagani, the former sweetheart of Paulita, arrived. Basilio told him not to get in the house but he was all but ignored. Basilio had no other choice but to let Isagani in on the secret, although having done that, Isagani still refused to heed Basilio.
Meanwhile, the Captain General observed that the lamp's glow was fading, and requested Father Irene to lift the wick. Isagani, quick as a lightning, rushed to the azotea, grabbed the lamp, and hurled it into the river. This done, Simoun's plan was thwarted. He hid in Father Florentino's house for he was being hunted down for investigation. In order to avoid arrest, Simoun poisoned himself. Before he died, he revealed to Father Florentino his real identity. He told the priest about the misery he had gone through since he came home from Europe, 13 years ago. He mentioned the love he and Maria Clara shared, and how he planned to cause an extensive riot by way of overthrowing the government.
In his desire to get rid of the jeweler's wealth, which was a tool for the latter's misdemeanor, Father Florentino flung the chest containing Simoun's wealth into the ocean, never to be unearthed.
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[noli me tangere]