Noli Me Tangere takes place in the Philippines during the time of Spanish colonization. In the opening scene, a wealthy and influential Filipino man named Captain Tiago hosts a dinner party to welcome Juan Crisóstomo Ibarra y Magsalin back to the Philippines. Ibarra has spent the last seven years studying in Europe. In talking to the various guests at Captain Tiago’s dinner party, he discovers that his father, Don Rafael, recently died, though he doesn’t know why or how. During the dinner, Father Dámaso, a loud-mouthed friar Ibarra has known since childhood, stands up and insults Ibarra, disparaging him for having traveled to Europe to pursue an education he could have obtained in the Philippines. In response, Ibarra swallows his pride and refrains from directing insults at the half-drunk friar. Instead, he leaves the dinner early, ignoring Captain Tiago’s plea that he stay a little longer in order to see his fiancée (and Captain Tiago’s daughter), María Clara.
On his way home, Ibarra walks with Señor Guevara, a lieutenant of the Civil Guard, Spain’s colonial armed forces that police the Philippines. The lieutenant explains that a few months after Ibarra left, Father Dámaso accused Don Rafael of not going to confession. Don Rafael was a very powerful man, which meant he had many enemies in both the Spanish government and in the church. The lieutenant tells Ibarra that one day Don Rafael came upon a government tax collector beating a boy in the street. When Rafael interfered, he accidentally pushed the man too hard, causing the tax collector to hit his head on a rock. This injury eventually led to the man’s death, and Ibarra’s father was thrown in jail and accused of subversion and heresy. At this point, Father Dámaso heaped new accusations on him and everybody abandoned him. By the time he was finally proven innocent, Guevara explains, Don Rafael had already died in prison.
Ibarra goes to his hometown, San Diego, where the unfortunate events of his father’s death took place. Since Captain Tiago owns multiple properties there, María Clara also relocates to San Diego. November is approaching, a time the town celebrates with a large festival. This festival is surrounded by various religious holidays, such as All Souls’ Day, which commemorates dead people in purgatory waiting for their souls to be cleansed before ascending to heaven. Taking advantage of this, San Diego’s priests implore the villagers to purchase indulgences, which they claim shorten the length of time a soul must languish in purgatory. Ibarra quickly sees that the power of the Catholic friars in the Philippines has greatly increased since he left for Europe, a fact made clear by their control over even governmental officials. For instance, Father Salví, San Diego’s new priest, is constantly at odds with the military ensign in charge of the village’s faction of the Civil Guard. Salví uses his important religious position to spite the ensign, fining the man for missing church services and delivering purposefully boring sermons when he does attend.
The friars interfere with other elements of everyday life in San Diego too, which Ibarra learns after speaking with the schoolmaster. The schoolmaster tells him that Father Dámaso actively meddles with his educational techniques by demanding that he teach only in the country’s native language, Tagalog, instead of instructing the children to speak Spanish. Dámaso also insists that the schoolmaster beat the children, creating a hostile environment that doesn’t lend itself to productive learning. Hearing this, Ibarra decides to build a secular school in San Diego, a project his father dreamed about before his death. On the advice of the town’s old philosopher, Tasio, Ibarra presents his ideas to the town’s religious and civic leaders, making it seem as if he wants them to be involved with the school, even though he plans to ignore their influence after it is built.
Meanwhile, two poor boys named Crispín and Basilio study to be sextons, or people who take care of the church. They do so in order to financially help their mother, Sisa, but Crispín is unfairly accused of theft and thus must work constantly with his brother to pay off the absurd amounts the chief sexton claims that Crispín owes the church. When he protests this injustice one night, Crispín is hauled away and severely beaten. Scared for his brother’s life, Basilio searches him out before running home during a storm and waiting in vain with his mother for Crispín to appear. This never materializes, and the next day Basilio goes back into town. Frightened, Sisa looks for both her boys and is told that the Civil Guard has been ordered to arrest them for theft, though nobody can find them. She herself is arrested and then released, at which point she searches throughout the night for her boys, working herself into permanent insanity and destitution as she wanders the town and the surrounding woods.
Visiting the Catholic cemetery, Ibarra speaks to a gravedigger and learns that, upon Father Dámaso’s orders, he dug up Don Rafael’s body. Although the friar had instructed the gravedigger to take Rafael’s body to the Chinese cemetery—a less respected cemetery—the gravedigger threw Don Rafael into the lake, thinking it a more honorable resting place.
Ibarra and the town’s influential religious and government leaders decide to celebrate the new school on the same day as the town’s fiesta. The church makes plans to bless the new educational building (though it is not yet completed) directly after a long sermon by Father Dámaso. During this sermon, a mysterious figure approaches Ibarra. His name is Elías, a man whose life Ibarra recently saved on an eventful fishing trip. Elías tells Ibarra that there is a plan to kill him during the school’s benediction ceremony, warning him not to walk beneath a certain large stone suspended by a pulley system. Ibarra ignores this advice, and sure enough, the stone hurdles toward him. Luckily Elías takes action and covertly puts the criminal—the man plotting against Ibarra—in the way of the stone, killing him instead of Ibarra. The festivities go on, but Ibarra now knows he has enemies.
That night, during a celebratory dinner hosted by Ibarra, Father Dámaso arrives uninvited. All of San Diego’s most respected individuals are in attendance, including the governor and the town’s other friars. Dámaso loudly insults the school and its architecture while also making callous remarks about “indios,” a racial slur for native Filipinos. He flippantly speaks about how “indios” abandon their country because they think they’re superior, traveling to Europe instead. “In this life the fathers of such vipers are punished,” he says. “They die in jail, eh, eh, or rather, they have no place…” When Ibarra hears Dámaso make this crude reference to his father’s unfair death, he jumps up and pins the priest down, holding a knife in his free hand and publicly accusing Dámaso of exhuming his father’s body. Ibarra says he won’t kill Dámaso, but his actions say otherwise, and as he lifts the knife to bury it in the friar’s body, María Clara snatches it from his hand.
In the aftermath of this scandalous event, Ibarra is excommunicated from the church. Captain Tiago proves himself a spineless socialite by calling off the wedding between Ibarra and María Clara, instead betrothing his daughter to Linares, a young man from Spain. Linares is the nephew of Don Tiburcio de Espadaña, a fraudulent doctor who treats María Clara for a sudden illness that incapacitates her for several days after the incident between Ibarra and Father Dámaso. Meanwhile, the Captain General—the topmost government official representing Spain—visits San Diego. The friars implore him to punish Ibarra, but because his priorities are more civic than religious and because he supports Ibarra’s mission to build a school, he pulls strings to have the young man’s excommunication lifted.
While Ibarra continues his project, Father Salví makes arrangements with a man named Lucas, the brother of the man hired to kill Ibarra with the large stone. Because his brother died, Lucas wants revenge on Ibarra. Father Salví—who secretly loves María Clara and who believes Ibarra is a heretic—hatches a plot with Lucas to frame Ibarra. With Lucas’s help, he organizes a band of rebels to attack the Civil Guard’s military barracks, telling them that Ibarra is the ringleader. Hours before the attack takes place, Father Salví rushes to the ensign and warns him of the plan, making sure to request that the ensign let it be known that he—Salví—was the one to save the town by discovering the plot and issuing a warning.
The attack goes according to Salví and Lucas’s plan, and Ibarra is arrested. He is imprisoned and found guilty, a verdict based on an ambiguous line in a letter he sent to María Clara. Once again Elías comes to the rescue, breaking him out of prison and taking him away in a boat. Before they leave town, Ibarra stops at María Clara’s house, climbs onto her patio, and says goodbye to her. She explains that she only parted with his letter—which led to his guilty sentencing—because she was blackmailed. Apparently, a man came to her and told her that her real father is Fray Dámaso, not Captain Tiago. The man threatened to spread this information if she didn’t give him Ibarra’s letter. Feeling that she must protect Captain Tiago’s honor and the memory of her deceased mother, she handed over Ibarra’s letter. Nonetheless, she tells Ibarra that she will always love him and that she is deeply sorry for having betrayed him.
After saying goodbye to María Clara, Ibarra gets into Elías’s boat. As the two men row into the night, they continue a heated discussion they’ve already begun about the nature of revolution and reform, debating the merits of working within a corrupt system to change it rather than overthrowing the system completely. As they talk, they realize they’re being chased by another boat. Elías tries to out-row their pursuers, but quickly realizes they’ll eventually catch up. As bullets whip by, he tells Ibarra to row, deciding to jump off the boat to confuse the people behind them. Before diving, he tells Ibarra to meet him on Christmas Eve in the woods near San Diego, where Ibarra’s grandfather is buried with the family’s riches. When Elías plunges into the water, the boat follows him instead of Ibarra. Elías throws them off by diving deep into the water, only surfacing periodically. Soon, though, the people chasing him don’t see him come back up. They even think they see a bit of blood in the water.
Back in San Diego, Father Dámaso visits María Clara, who tells him she can’t marry Linares because she doesn’t love him. She references a newspaper, which falsely reported that Ibarra was found dead on the banks of the lake. She tells the friar that this news has given her no reason to live and, as such, she can’t go through with the wedding, instead deciding to enter a convent.
On Christmas Eve, the young Basilio wanders forth from a cabin in the woods, where he’s been living with a kind family ever since the Civil Guard started looking for him. He goes into San Diego in search of Sisa, his mother. When he finds her, she doesn’t recognize him and runs away, leading him back to the woods, where she goes to the old tomb that contains Ibarra’s grandfather. Once he finally catches up to his mother, though, Basilio faints. Seeing finally that he is her son, Sisa covers him with kisses. When Basilio wakes up, he finds that she has died by his side. At that moment, Elías appears. He is wounded, and seeing that Ibarra has not arrived, he tells Basilio he is about to die, instructing the boy to burn his and Sisa’s bodies on a pyre. Looking up at the sky, he utters his final words: “I die without seeing dawn’s light shining on my country…You, who will see it, welcome it for me…don’t forget those who fell during the nighttime.” The book ends without mention of Ibarra’s fate.