Characters of El Fili

* Simoun - Crisostomo Ibarra in disguise, left for dead at the end of Noli Me Tangere, has resurfaced as the wealthy jeweler, Simoun, now sporting a beard, blue-tinted glasses, and a revolver. Fueled by his mistreatment at the hands of the Spaniards and his fury at Maria Clara's fate, he has since shed his pacifist image and become the titular "filibustero", pretending to side with the upper class and encouraging them to enslave the masses, while in reality siding with the masses and urging them to revolt against the oppressive Spanish regime. This time, he does not attempt to fight the authorities with knowledge, but by force. He concocts a plot to set off a bomb disguised as a beautiful lamp at a wedding where important members of civil society and the church hierarchy are in attendance. Unfortunately for him, his plan fails and he commits suicide by consuming poison.

* Basilio - After the tragic deaths of his mother and younger brother, Basilio heeds the advice of the dying boatman, Elias, and travels to Manila to study. At first he is frowned upon by his peers and teachers not only because of the color of his skin but also because of his shabby appearance, but redeems himself in their eyes by participating in a fencing contest--and winning. He soon becomes an exceptional medical student, but his plans to graduate and become a full-time doctor are postponed by an encounter with Simoun, who, upon bringing up the deaths of his relatives, convinces him to aid him in his plots. At first, the young man is reluctant, but the death of his sweetheart Juliana drives him to fight wholeheartedly by Simoun's side. He helps Simoun smuggle in a bomb into a wedding reception, but relents later on and warns his best friend Isagani of the impending danger.

* Isagani - Basilio's best friend. While Basilio is an aspiring doctor, Isagani, on the other hand, is a budding poet, and he, along with Basilio, plans to establish a school wherein indios such as themselves may learn Spanish. Unlike Basilio, he does not get along well with Simoun, and is much more emotional and reactive than his friend. Isagani experiences a rocky relationship with his rich girlfriend, Paulita Gomez, who eventually dumps him and marries Isagani's fellow student, Juanito Pelaez. Heartbroken, Isagani refuses at first to listen to Basilio when the latter warns him to get away from the would-be epicenter of the explosion, but eventually foils Simoun's plan, racing into the reception in time to prevent the explosion from happening.