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.