Crisóstomo Ibarra, the mestizo son of the recently deceased Don Rafael Ibarra, is returning to San Diego in Laguna after seven years of study in Europe. Kapitán Tiago, a family friend, bids him to spend his first night in Manila where Tiago hosts a reunion party at his riverside home on Anloague Street. Crisóstomo obliges. At dinner he encounters old friends, Manila high society, and Padre Dámaso, San Diego's old curate at the time Ibarra left for Europe. Dámaso treats Crisóstomo with hostility, surprising the young man who always viewed the friar to be a family friend. Crisóstomo excuses himself early and is making his way back to his hotel when Lieutenant Guevarra, another friend of his father, catches up with him. As the two of them walk to Crisóstomo's stop, and away from the socialites at the party who may possibly compromise them if they heard, Guevarra reveals to the young man the events leading up to Rafael's death and Dámaso's role in it. Crisóstomo, who has been grieving from the time he learned of his father's death, decides to forgive and not seek revenge. Guevarra nevertheless warns the young man to be careful. The following day, Crisóstomo returns to Kapitán Tiago's home in order to meet with his childhood sweetheart, Tiago's daughter María Clara. The two flirt and reminisce in the azotea, a porch overlooking the river. María reads back to Crisóstomo his farewell letter wherein he explained to her Rafael's wish for Crisóstomo to set out, to study in order to become a more useful citizen of the country. Seeing Crisóstomo agitated at the mention of his father, however, María playfully excuses herself, promising to see him again at her family's San Diego home during the town fiesta. Crisóstomo goes to the town cemetery upon reaching San Diego to visit his father's grave. However, he learns from the groundskeeper that the town curate had ordered that Rafael's remains be exhumed and transferred to a Chinese cemetery. Although Crisóstomo is angered at the revelation, the groundskeeper adds that on the night he dug up the corpse, it rained hard and he feared for his own soul, causing him to take pity on Rafael and instead defy the curate's orders by throwing the body into the lake. At that moment, Padre Bernardo Salví, the new curate of San Diego, walks into the cemetery. Crisóstomo's anger explodes as he shoves him into the ground and demands an accounting; Salví fearfully tells Crisóstomo that the transfer was ordered by the previous curate, Padre Dámaso, causing the latter to leave in consternation. Crisóstomo, committed to his patriotic endeavors, is determined not to seek revenge and to put the matter behind him. As the days progress he carries out his plan to serve his country as his father wanted. He intends to use his family wealth to build a school, believing that his paisanos would benefit from a more modern education than what is offered in the schools run by the government, whose curriculum was heavily tempered by the teachings of the friars. Enjoying massive support, even from the Spanish authorities, Crisóstomo's preparations for his school advance quickly in only a few days. He receives counsel from Don Anastacio, a revered local philosopher, who refers him to a progressive schoolmaster who lamented the friars' influence on public education and wished to introduce reforms. The building was planned to begin construction with the cornerstone to be laid in a ceremony during San Diego's town fiesta. One day, taking a break, Crisóstomo, María, and their friends get on a boat and go on a picnic along the shores of the Laguna de Baý, away from the town center. It is then discovered that a crocodile had been lurking on the fish pens owned by the Ibarras. Elías, the boat's pilot, jumps into the water with a bolo knife drawn. Sensing Elías is in danger, Crisóstomo jumps in as well, and they slaughter the animal together. Crisóstomo mildly scolds the pilot for his rashness, while Elías proclaims himself in Crisóstomo's debt. On the day of the fiesta, Elías warns Crisóstomo of a plot to kill him at the cornerstone-laying. The ceremony involved the massive stone being lowered into a trench by a wooden derrick. Crisóstomo, being the principal sponsor of the project, is to lay the mortar using a trowel at the bottom of the trench. As he prepares to do so, however, the derrick fails and the stone falls into the trench, bringing the derrick down with it in a mighty crash. When the dust clears, a pale, dust-covered Crisóstomo stands stiffly by the trench, having narrowly missed the stone. In his place beneath the stone is the would-be assassin. Elías has disappeared. The festivities continue at Crisóstomo's insistence. Later that day, he hosts a luncheon to which Padre Dámaso gatecrashes. Over the meal, the old friar berates Crisóstomo, his learning, his journeys, and the school project. The other guests hiss for discretion, but Dámaso ignores them and continues in an even louder voice, insulting the memory of Rafael in front of Crisóstomo. At the mention of his father, Crisóstomo strikes the friar unconscious and holds a dinner knife to his neck. In an impassioned speech, Crisóstomo narrates to the astonished guests everything he heard from Lieutenant Guevarra, who was an officer of the local police, about Dámaso's schemes that resulted in the death of Rafael. As Crisóstomo is about to stab Dámaso, however, María Clara stays his arm and pleads for mercy. Crisóstomo is excommunicated from the church, but has it lifted through the intercession of the sympathetic governor general. However, upon his return to San Diego, María has turned sickly and refuses to see him. The new curate whom Crisóstomo roughly accosted at the cemetery, Padre Salví, is seen hovering around the house. Crisóstomo then meets the inoffensive Linares, a peninsular Spaniard who, unlike Crisóstomo, had been born in Spain. Tiago presents Linares as María's new suitor. Sensing Crisóstomo's influence with the government, Elías takes Crisóstomo into confidence and one moonlit night, they secretly sail out into the lake. Elías tells him about a revolutionary group poised for an open and violent clash with the government. This group has reached out to Elías in a bid for him to join them in their imminent uprising. Elías tells Crisóstomo that he managed to delay the group's plans by offering to speak to Crisóstomo first, that Crisóstomo may use his influence to effect the reforms Elías and his group wish to see. In their conversation, Elías narrates his family's history, how his grandfather in his youth worked as a bookkeeper in a Manila office but was accused of arson by the Spanish owner when the office burned down. He was prosecuted and upon release was shunned by the community as a dangerous lawbreaker. His wife turned to prostitution to support the family but were eventually driven into the hinterlands. Crisóstomo sympathizes with Elías, but insists that he could do nothing, and that the only change he was capable of was through his schoolbuilding project. Rebuffed, Elías advises Crisóstomo to avoid any association with him in the future for his own safety. Heartbroken and desperately needing to speak to María, Crisóstomo turns his focus more towards his school. One evening, though, Elías returns with more information – a rogue uprising was planned for that same night, and the instigators had used Crisóstomo's name in vain to recruit malcontents. The authorities know of the uprising and are prepared to spring a trap on the rebels. In panic and ready to abandon his project, Crisóstomo enlists Elías in sorting out and destroying documents in his study that may implicate him. Elías obliges, but comes across a name familiar to him: Don Pedro Eibarramendia. Crisóstomo tells him that Pedro was his great-grandfather, and that they had to shorten his long family name. Elías tells him Eibarramendia was the same Spaniard who accused his grandfather of arson and was thus the author of the misfortunes of Elías and his family. Frenzied, he raises his bolo to smite Crisóstomo, but regains his senses and leaves the house very upset. The uprising follows through, and many of the rebels are either captured or killed. They point to Crisóstomo as instructed and Crisóstomo is arrested. The following morning, the instigators are found dead. It is revealed that Padre Salví ordered the senior sexton to kill them in order to prevent the chance of them confessing that he actually took part in the plot to frame Crisóstomo. Elías, meanwhile, sneaks back into the Ibarra mansion during the night and sorts through documents and valuables, then burns down the house. Some time later, Kapitán Tiago hosts a dinner at his riverside house in Manila to celebrate María Clara's engagement with Linares. Present at the party were Padre Dámaso, Padre Salví, Lieutenant Guevarra, and other family friends. They were discussing the events that happened in San Diego and Crisóstomo's fate. Salví, who lusted after María Clara all along, says that he has requested to be transferred to the Convent of the Poor Clares in Manila under the pretense of recent events in San Diego being too great for him to bear. A despondent Guevarra outlines how the court came to condemn Crisóstomo. In a signed letter, he wrote to a certain woman before leaving for Europe, Crisóstomo spoke about his father, an alleged rebel who died in prison. Somehow this letter fell into the hands of an enemy, and Crisóstomo's handwriting was imitated to create the bogus orders used to recruit the malcontents to the San Diego uprising. Guevarra remarks that the penmanship on the orders was similar to Crisóstomo's penmanship seven years before, but not at the present day. And Crisóstomo had only to deny that the signature on the original letter was his, and the charge of sedition founded on those bogus letters would fail. But upon seeing the letter, which was the farewell letter he wrote to María Clara, Crisóstomo apparently lost the will to fight the charges and owned the letter as his. Guevarra then approaches María, who had been listening to his explanation. Privately but sorrowfully, he congratulates her for her common sense in yielding Crisóstomo's farewell letter. Now, the old officer tells her, she can live a life of peace. María is devastated. Later that evening Crisóstomo, having escaped from prison with the help of Elías, climbs up the azotea and confronts María in secret. María, distraught, does not deny giving up his farewell letter, but explains she did so only because Salví found Dámaso's old letters in the San Diego parsonage, letters from María's mother who was then pregnant with María. It turns out that Dámaso was María's biological father. Salví promised not to divulge Dámaso's letters to the public in exchange for Crisóstomo's farewell letter. Crisóstomo forgives her, María swears her undying love, and they part with a kiss. Crisóstomo and Elías escape on Elías's boat. They slip unnoticed through the Estero de Binondo and into the Pasig River. Elías tells Crisóstomo that his treasures and documents are buried in the middle of a forested land owned by the Ibarras in San Diego. Wishing to make restitution, Crisóstomo offers Elías the chance to escape with him to a foreign country, where they will live as brothers. Elías declines, stating that his fate is with the country he wishes to see reformed and liberated. Crisóstomo then tells him of his own desire for revenge and revolution, to lengths that even Elías was unwilling to go. Elías tries to reason with him, but sentries catch up with them at the mouth of the Pasig River and pursue them across Laguna de Bay. Elías orders Crisóstomo to lie down and to meet with him in a few days at the mausoleum of Crisóstomo's grandfather in San Diego, as he jumps into the water in an effort to distract the pursuers. Elías is shot several times. The following day, news of the chase were in the newspapers. It is reported that Crisóstomo, the fugitive, had been killed by sentries in pursuit. At the news, María remorsefully demands of Dámaso that her wedding with Linares be called off and that she be entered into the cloister, or the grave. Seeing her resolution, Dámaso admits that the true reason that he ruined the Ibarra family and her relationship with Crisóstomo was because he was a mere mestizo and Dámaso wanted María to be as happy as she could be, and that was possible only if she were to marry a full-blooded peninsular Spaniard. María would not hear of it and repeated her ultimatum, the cloister or the grave. Knowing fully why Salví had earlier requested to be assigned as chaplain in the Convent of the Poor Clares, Dámaso pleads with María to reconsider, but to no avail. Weeping, Dámaso consents, knowing the horrible fate that awaits his daughter within the convent but finding it more tolerable than her suicide. A few nights later in the forest of the Ibarras, a boy pursues his mother through the darkness. The woman went insane with the constant beating of her husband and the loss of her other son, an altar boy, in the hands of Padre Salví. Basilio, the boy, catches up with Sisa, his mother, inside the Ibarra mausoleum in the middle of the forest, but the strain had already been too great for Sisa. She dies in Basilio's embrace. Basilio weeps for his mother, but then looks up to see Elías staring at them. Elías was dying himself, having lost a lot of blood and having had no food or nourishment for several days as he made his way to the mausoleum. He instructs Basilio to burn their bodies and if no one comes, to dig inside the mausoleum. He will find treasure, which he is to use for his own education. As Basilio leaves to fetch the wood, Elías sinks to the ground and says that he will die without seeing the dawn of freedom for his people and that those who see it must welcome it and not forget them that died in the darkness. In the epilogue, Padre Dámaso is transferred to occupy a curacy in a remote town. Distraught, he is found dead a day later. Kapitán Tiago fell into depression and became addicted to opium and is forgotten by the town. Padre Salví, meanwhile, awaits his consecration as a bishop. He is also the head priest of the convent where María Clara resides. Nothing is heard of María Clara; however, on a September night, during a typhoon, two patrolmen reported seeing a specter (implied to be María Clara) on the roof of the Convent of the Poor Clares moaning and weeping in despair. The next day, a representative of the authorities visited the convent to investigate previous night's events and asked to inspect all the nuns. One of the nuns had a wet and torn gown and with tears told the representative of "tales of horror" and begged for "protection against the outrages of hypocrisy" (which gives the implication that Padre Salví regularly rapes her when he is present). The abbess however, said that she was nothing more than a madwoman. The General also attempted to investigate the nun's case, but by then the abbess prohibited visits to the convent. Nothing more was said again about María Clara.
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