Having completed his studies in Europe, young Juan Crisostomo Ibarra y Magsalin came back to
the Philippines after 7 years. In his honor, Don Santiago, a family friend also known as Capitan
Tiago, threw a get-together party, which was attended by friars and other prominent figures. One
of the guests, former San Diego curate Father Damaso belittled and slandered Ibarra. Ibarra
brushed off the insults and took no offense; he instead politely excused himself and left the party
because of an allegedly important task.
The next day, Ibarra visits Maria Clara, his fiancée, the beautiful daughter of Captain Tiago.
Before Ibarra left for San Diego, Lieutenant Guevara, a guardia civil, reveals to him the death of
his father, Don Rafael Ibarra. According to Guevara, Don Rafael was unjustly accused of being a
heretic, in addition to being a filibustero an allegation brought forth by Father Damaso because
of Don Rafael's non-participation in the Sacraments, such as Confession and Mass. Father
Damaso's hatred against Ibarra's father is provoked by another incident when Don Rafael helped
out on a fight between a tax collector and a child fighting, and the former's death was blamed on
him, although it was not deliberate. Suddenly, all of those who thought ill of him surfaced with
additional complaints. He was imprisoned, and just when the matter was almost settled, he got
sick and died in jail. Still not content with what he had done, Damaso arranged for Don Rafael's
corpse to be dug up from the Catholic church and brought to a Chinese cemetery, because he
thought it inappropriate to allow a heretic in a Catholic burial ground. Unfortunately, it was
raining and because of the bothersome weight of the body, the undertakers decided to throw the
corpse into a nearby lake.
Revenge was not in Ibarra's plans; instead he carried through his father's plan of putting up a
school, since he believed that education would pave the way to his country's progress.
During the inauguration of the school, a suspicious accident happen that aimed Ibarra’s life. He
would have been killed in sabotage if it wasn’t for Elias, a mysterious man who had warned
Ibarra. The festivities proceed until the dinner, where Ibarra is insulted over the memory of his
father by Father Damaso. Ibarra loses control of himself and is about to kill the friar, who is
saved by the intervention of Maria Clara.
Ibarra is excommunicated, and Capitan Tiago, through his fear of the friars, is forced to break the
engagement and agree to the marriage of Maria Clara with a young Spaniard provided by Father
Damaso. Obedient to her reputed father’s command and influenced by her mysterious dread of
Padre Salvi, Maria Clara consents to this arrangement, but got seriously ill but was luckily cured
by the medicine Ibarra sent.
With the help of the Captain-General, Ibarra's excommunication was nullified and the
Archbishop decided to accept him as a member of the Church once again. But, as fate would
have it, some incident of which Ibarra had known nothing about was blamed on him, and he is
wrongly arrested and imprisoned. The accusation against him was then overruled because during
the litigation that followed, nobody could testify that he was indeed involved.
Meanwhile, in Capitan Tiago's residence, a party was being held to announce the upcoming
wedding of Maria Clara and Linares. Ibarra, with the help of Elias, took this opportunity to
escape from prison. Before leaving, Ibarra spoke to Maria Clara and accused her of betraying
him, thinking that she gave the letter he wrote her to the jury. Maria Clara explained that she
would never conspire against him, but that she was forced to surrender Ibarra's letter to Father
Salvi, in exchange for the letters written by her mother even before she was born. The letters of
her mother were addressed to Father Damaso about their unborn child which means that she is
the biological daughter of the priest and not of her father, Capitan Tiago. She tells him that she
will marry the young Spaniard, sacrificing herself thus to save her mother’s name and Capitan
Tiago’s honor and to prevent a public scandal, but that she will always remain true to him.
Ibarra and Elias flee to the lake and were chased by the Guardia Civil. One was shot and the
other survives. Upon hearing the news, Maria Clara believed that Ibarra was dead; she entered
the nunnery instead of marrying Alfonso Linares.
The fatally wounded Elias found the child Basilio and his dead mother Sisa who was driven to
insanity when she learned that her children were implicated for theft by the sacristan mayor.
Elias instructed Basilio to dig for his and Sisa’s graves and there is a buried treasure which he
can use for his education.
In the end, Capitan Tiago became addicted to opium. Maria Clara became a nun where Father
Salvi, who has lusted over Maria Clara from the beginning, regularly used her to fulfill his lust.
One stormy evening, a beautiful crazy woman was seen at the top of the convent crying and
cursing the heavens for the fate it has handed her. While the woman was never identified, it is
suggested that the said woman was Maria Clara.
