Something I've hardly seen people discuss is that the two people in the novel that Ibarra comes to cherish most (Maria Clara & Elias) are character foils — and also representative of Ibarra's mindset regarding the country.
Because Maria Clara is a rich spanish (not technically Spanish, but is essentially treated like one) woman who is favored by the priests and is praised as the epitome of Spanish Artistocracy.
Meanwhile, Elias is the fugitive, the outcast, the rebel, the one who is constantly on the run and whose whole life was ruined by said Spanish Artistocracy.
Essentially, Maria Clara and Elias represent two main concepts: Submission vs Subversion.
And in the beginning of the novel, before meeting Elias, Ibarra gravitates towards submission. He has everything. He himself has benefited from this artistocratic system— in his eyes, there is no reason to rebel, because his life is essentially perfect. He is about to get married, start a school, chase his dreams.
But then, his life starts to crumble. He gets into a scuffle with Father Salvi. His plans for construction/education are constantly being ruined by the priests. He attempts to kill Father Damaso and is excommunicated.
So in the end, he is forced to leave. He is forced to run away, he is forced to leave Maria Clara and run away with Elias — he is forced to leave his submission, to open his eyes to the horrors of the system that Elias had challenged on the boat. He is forced to leave his fiance — and with leaving Maria, he is forced to realize that the country needs a change. He is forced to set beside his submission become subversive, because in the end, submission did not even work with Maria Clara herself.
