The novel centers on the Noli-El Fili duology's main character Crisóstomo Ibarra, now returning for vengeance as "Simoun".

The novel's dark theme departs dramatically from the previous novel's hopeful and romantic atmosphere, signifying Ibarra's resort to solving his country's issues through violent means, after his previous attempt in reforming the country's system made no effect and seemed impossible with the corrupt attitude of the Spaniards toward the Filipinos.

Both of Rizal's novels had a profound effect on Philippine society in terms of views about national identity, the Catholic faith and its influence on the Filipino's choice, and the government's issues in corruption, abuse of power, and discrimination, and on a larger scale, the issues related to the effect of colonization on people's lives and the cause for independence.

In the events of the previous novel, Crisóstomo Ibarra, a reform-minded mestizo who tried to establish a modern school in his hometown of San Diego and marry his childhood sweetheart, was falsely accused of rebellion and presumed dead after a shootout following his escape from prison.

At Barrio Sagpang in the town of Tiani, Simoun stays at the house of the village's cabeza de barangay, Tales.

During the Quiapo Fair, a talking heads[3] exhibit[4] ostensibly organized by an American named Mr. Leeds but secretly commissioned by Simoun is drawing popular acclaim.

The exhibit is set in Ptolemaic Egypt but features a tale that closely resembled that of Crisóstomo Ibarra and María Clara, and their fate under Salví.

Deeply overcome with guilt and fear, Salví recommends the show be banned, but not before Mr. Leeds sailed for Hong Kong.

However, Basilio reports to Simoun that María Clara died just that afternoon, after suffering the travails of monastic life under Salví, who always lusted after her.

During his imprisonment, he learns that Capitán Tiago has died, leaving him with nothing; it is revealed that Tiago's will was actually forged by his spiritual advisor Padre Írene, who also supplied him with opium; his childhood sweetheart Juli has committed suicide to avoid getting raped by parish priest Camorra when she tried asking for help on Basilio's behalf; and that he has missed his graduation and will be required to study for another year, but now with no funds to go by.

As the Peláez and Gómez families are prominent members of the Manila elite, leaders of the church and civil government are invited to the reception.

At the sound of the explosion, Simoun's mercenaries will attack, reinforced by Matanglawin and his bandits who will descend upon the city from the surrounding hills.

He discovers that this was to be the reception venue – Juanito Peláez's father bought Tiago's house as a gift for the newlywed couple.

One day, the lieutenant of the local Guardia Civil informs Florentino that he received an order to arrest Simoun that night.

Retrieving some of his family's treasure that Elias had buried in the Ibarra mausoleum in the forest, Crisóstomo fled to foreign lands and engaged in trade.

Once in the country, Crisóstomo then used him as a blind tool and incited him to all kinds of injustice, taking advantage of the Captain-General's insatiable lust for gold.

Realizing that the arresting officers will confiscate Crisóstomo's possessions, Florentino divests him of his jewels and casts them into the sea, proclaiming that they are best hidden under the waters for the time being to ensure that they cannot be used to distort justice or incite greed, and that God shall provide the means to draw them out should people need wealth for a righteous cause.