It is 1917. Portugal is feeling the after-effects of a storm of anti-religious sentiment and the violent overthrow of the monarchy and the government in the 5 October 1910 revolution. Churches in Lisbon and the rest of Portugal are boarded up. Many priests, nuns, monks and friars are shown being fingerprinted, photographed and registered as possible criminals before being jailed. The rural town of Fátima is small enough to have escaped much of this persecution; their church remains open, and most of the people are reasonably devout. Watching their flocks and playing in a field outside town on May 15, Lúcia Santos and her cousins, Jacinta Marto and Francisco Marto decide to pray their version of the Rosary by yelling out, "Hail Mary!" but not finishing the prayer. In the midst of this activity they hear a clap of thunder and see a flash of lightning from a distance. Thinking it is about to rain, the children gather their sheep and head for their homes. Another flash of lightning causes them to run straight into an unusual "cloud of light" surrounding a little tree on which a mysterious lady stands. Speaking slowly and gently, the Lady asks them to return on the 13th of each month and to offer their sufferings to God for the salvation of sinners. She entreats them to say the Rosary for world peace. Later, they encounter their agnostic friend Hugo who tells them it is best not to reveal the vision to anyone else, but of course on returning home, Jacinta immediately divulges her sightings. Jacinta and Francisco's parents quickly believe the story, but Lúcia's mother reacts with disgust and subjects her daughter to emotional and physical mistreatment. She forbids Lúcia to return to the Cova da Iria, but Lúcia does so anyway on the next month's appearance, and is told then that her cousins will die and go to heaven "soon", while she will live a long life in holy service. The parish priest suggests the visions might be from Satan. The local authorities close the Fátima church until the priest can convince the parishioners that no visions have or will happen. The next month, on July 13, the Lady appears again, predicting "another and worse war" will happen if the world doesn't stop sinning. She also predicts evil will come from Russia if that nation is unconverted. Kidnapped by provincial administrator Artur Santos, the children are first offered bribes, then threatened with death if they don't change their story. Trying to frighten them, he has first Jacinta, then Francisco dragged into another room. Jacinta's terrified screams convince Lúcia that her cousins are dead, but she refuses to deny what she's seen. Warning her that she's about to experience "the full treatment", Artur Santos reunites her with her cousins, who are very much alive, then throws them all in jail. There they find Hugo, who stands by them as they convince all the prisoners to join in the Rosary. Unable to find any prosecutable evidence, Artur frees the children, who find that the entire population of Fátima has been standing outside waiting for them. On October 13, when the Lady promised "a sign that will make them believe", about forty thousand people arrive, waiting through a torrential downpour. The Lady appears and says that the war will be over soon and the soldiers will be returning to their homes. At precisely noon, as the Lady raises her hands, the clouds part and the sunlight shines brightly upon all the people—then the Sun shifts through a rainbow of colours and appears to move closer, in what many have described as the miracle of the Sun. Many people panic, some pray or watch calmly, and a few sick and disabled people are healed. As the Sun returns to normal, we see Hugo standing in the middle of the kneeling crowd, his hat still on. Removing it, he says "Only the fool sayeth there is no God." A short epilogue, circa 1951, shows the huge basilica where the tree once stood and a million people outside paying homage to Our Lady of Fátima. At the end of the film, inside the new basilica, Lúcia is now a nun praying before the tomb where her cousins are buried, with the converted Hugo at her side.
