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In 1917, Mexico is being governed by a military general who outlaws religion and sends his soldiers to seek out and kill all priests. Meanwhile, in a Catholic seminary, novice Miguel Pro has doubts about his vocation, because he fears that his exuberant, mischievous nature is not in keeping with the dignity of the priesthood. However, his teacher encourages him, as Miguel brings so much joy to others through his singing and joking. When soldiers approach the seminary, intent on destruction, the superior sends his students home after telling them to await instruction. Taking refuge with a sympathetic couple living nearby, Miguel trades his good suit for the man's peasant clothes, in order to disguise himself during the journey home. At his mother's house, his sister Ana and two brothers, Humberto and Roberto, encourage Miguel to give up the seminary and warn him that the general has placed Colonel Amadeo Marinos in charge of a special police force that is tracking down all priests and seminarians. Miguel feels obligated to continue his studies, but suggests a joke to play on the tormenters. This annoys the impetuous Humberto, who says that they must fight repression with bombs. Miguel confides in his mother that he has doubts about being an intermediary between God and the people, but she tells him that he is needed because he makes others happy. A young neighbor, Luis Vilches, delivers a message from the seminary stating that arrangements have been made to send Miguel to California to complete his religious training, but Miguel still feels unsure about his fitness to be a priest. That night, as he is thinking hard about his decision, he witnesses soldiers killing the local bishop. Although Miguel is unable to save the man, he later tells Humberto that he is now sure of his vocation. In the following years, while Miguel is out of the country, the general, claiming there is no God, continues his persecution of Catholics, forcing them to worship in secret. When Joe Weiler, a New York reporter, comes to Mexico to cover events for his newspaper, the general brags that he has made Mexico modern and strong and that the people, who are now free to think for themselves, are behind his efforts. Doubting him, Weiler gains his permission to travel around the country and see for himself. After his ordination, Miguel returns to his mother's home, only to learn that she has died and that his siblings have relocated to Mexico City because of trouble with the authorities. Luis, now grown, finds Miguel and takes him to his mother's grave, where the police, who were alerted by the woman now living in his mother's house, try unsuccessfully to capture him. When Luis takes Miguel to a saloon that is owned and patronized by Catholics, he is asked to hold a secret Mass, baptize the children and officially marry their parents. Miguel is honored to oblige, although Luis warns Miguel that performing the Catholic sacraments puts everyone at risk, including his friends and family. Upon reuniting with Ana and Roberto, Miguel learns that Humberto, who is a member of the Religious Defense League, has been imprisoned on suspicion of dissident behavior. To see Humberto, Miguel disguises himself as a police inspector and brazenly enters the jail, where Carlos Larrea, the police captain, recognizes him. However, to the priest's surprise, Larrea quietly asks him to hold a Mass for his family. When Humberto is released the following day, a policeman who saw Larrea and Miguel together reports his suspicions to Marinos and identifies Miguel from a photograph the colonel has obtained. Through word of mouth, other people, hungry for their religion, ask for Miguel's services. Soldiers, who get news from paid informants, track Miguel to a farm where he has baptized several children, but Miguel slips past them by donning a disguise. Humberto then drives up in a car given to him by the League and tries to dissuade Miguel from performing a Mass for four hundred people, arguing that a secret cannot be kept by so many people. Miguel gives no thought to the danger and the Mass goes smoothly, but Weiler is present, and when his New York paper prints a story about it, the infuriated general wants Miguel dead. As he goes about his priestly work, Miguel gives aid whenever he can, helping to find homes for orphans and food for the poor, prompting a nun to tell him that his presence is like having rain during a dusty summer. Meanwhile, Marinos circulates Miguel's photographs to the entire police force and orders the men to memorize it. After learning that Larrea has been arrested, Humberto warns Miguel that they are a danger to everyone they know. When Miguel answers a summons from an old family friend, the wealthy Señora Altera, Marinos is on his trail. Although one of their friends, Margarita, convinces the colonel that Miguel has not been there, an old man intercepts the colonel to tell him that Miguel is at Altera's home. Marinos searches the premises, but finds no one except a hard-of-hearing woman whom the Señora claims is her visiting sister, and does not recognize that the woman is actually Miguel incognito. Afterward, Humberto urges Miguel to return to California, but the priest feels he is needed in Mexico. Later, when a policeman recognizes Miguel, the priest evades him by asking for help from the prostitute Laurette, who leads him to her apartment, arm in arm, causing the policeman to doubt himself. Later, the rash Luis suggests that they can solve the country's problems by assassinating the general, but Miguel and even Humberto, who has matured over the years, are against the idea. Accusing them of cowardice, Luis leaves in anger, but Humberto assures Miguel that Luis will not act out his violent thoughts. However, refusing to heed his friends, Luis drives past the general in Humberto's car and tosses a bomb. He is caught before the general comes to harm, but Humberto and Miguel become implicated in the attempted killing because of the car. Knowing they are in grave danger, Humberto wants to leave the city, but Miguel, who has promised to attend a family's dying grandmother, agrees to meet Humberto and Roberto later. Although soldiers burst into the grieving family's house and fail to find him, Miguel and his brothers are later captured. The general orders Marinos to arrange a peremptory trial and then execute the brothers, but the colonel, who is having a change of heart, argues that a summary execution will reflect badly on their leadership. Interested in Miguel, the general has the priest brought to him and offers to free them, if Miguel promises to give up the priesthood. Miguel refuses, but asks that his brothers be released. The general says that Roberto can go free, but the politically active Humberto will be executed at his side. On the day of their execution, Marinos asks for, and is granted, Miguel's forgiveness. When it is time to die, Miguel, refusing a blindfold, stretches out his arms in the form of the cross. After the execution, thirty thousand mourners join his funeral procession. The general, watching from his balcony, predicts that the people will soon forget about the priest, but Marinos and Weiler remain skeptical.