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In a Latin American village, a priest dressed in ragged peasant clothes seeks shelter in an abandoned church and is discovered praying by Maria Dolores, an Indian.  The priest confesses to Maria that he used to be the village's spiritual leader, but is now being pursued by the police, who are acting on government orders to eradicate all religious figures.  Although the law forbids public religious acts, the priest tells Maria he will baptize her illegitimate baby as well as all the other un-baptized babies in the village.  The ceremony is well attended by candle-bearing worshippers, and many children, including Maria's, are baptized.

At the port city of Puerto Grande, meanwhile, American fugitive James Calvert, known as "El Gringo," disembarks with a satchel of stolen money.  While Calvert, who is wanted for murder, fades into a crowd, a police lieutenant confers with the local chief of police about the priest.  The Chief shows the Lieutenant a photograph of the priest, who is the only remaining padre in the country, and the zealous lieutenant vows to kill the priest before the "rains come."  To achieve his goal, the Lieutenant plans to take and kill hostages from every village until the priest is turned over to him.  Leading an army of men, the Lieutenant, who believes that religion exploits poor people, then descends on the priest's village.  Although the priest offers himself, the Lieutenant fails to recognize him and insists on taking a married man as his hostage.

Terrified, the priest heads for Puerto Grande, intending to leave the country on the next boat.  Along the way, he is accosted by a beggar, who discovers a poster with the priest's photograph printed on it and pursues him.  The beggar insists on accompanying the priest and, while the padre sleeps in a cave, drinks his consecrated wine.  Unnerved by the beggar, the priest runs off and eventually arrives in Puerto Grande.

As he is about to board a ship, however, a young boy asks him to say mass for his dying mother.  Reluctantly the priest misses the boat to attend to the woman, but is unable to say mass because he has no wine, which is illegal.  Accompanied by the boy, the priest sets out to buy wine on the black market and is soon negotiating with the Governor's cousin.  The cousin and a corrupt police sergeant insist that the priest join them for a drink, and before long, the bottle is emptied.

In a panic, the priest grabs a bottle of brandy and rushes into the street, where he is caught by the police and jailed.  Once again, the Lieutenant fails to recognize the priest, and the Governor's cousin sets him free.  Having seen the hostage being marched to a firing squad, the priest returns to his village and is hounded by the beggar.  Maria advises the priest to cross the mountains to safety but, exhausted, he falls asleep at the cantina where she works.

When the police arrive, Maria dances for them to give the priest time to flee. The Lieutenant, who is the father of Maria's child, then rides up and chases both the priest and Calvert into a corn field.  Calvert engages the police in a gunfight, enabling the priest to escape to a sanctuary state while being wounded himself.

Soon after, the beggar turns up with a note he claims was written by a dying Calvert, asking the priest to hear the criminal's confession.  Although the priest doubts the beggar, he follows him back across the border.  In his hideout, Calvert denies writing the note, and the priest is captured by the police.  The Lieutenant offers the priest his life on condition he renounce his faith, but the priest refuses.  While being led to the firing squad, the priest tells the guilt-ridden beggar to give his ill-gotten money to the poor and faces his death with newfound courage.  As the priest is shot, the Lieutenant clutches his chest in repentant sorrow, unaware that back in the priest's church, another man of God has come to pray.