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In 1769, Don Gaspar de Portola and his friend, Lt. José Mendoza, travel by carriage to Mexico City, New Spain. At their insistence, the carriage travels so fast that it hits an old woman and kills her. Padre Junípero Serra gives the woman last rites and then chastises the soldiers for their carelessness. Upon arriving at their destination, the soldiers are given orders to occupy California, which, although discovered by the Spanish in 1536, has not yet been conquered. The soldiers also hope to discover the legendary Seven Cities of Gold. Two parties are dispatched by sea, and an advance group takes an overland route to San Diego Bay. The main expedition, commanded by Portola, is ordered to meet the other three parties at San Diego and then proceed northward to Monterey Bay. Padre Serra, who hopes to found a string of missions in California, is named spiritual director of the expedition. As he blesses the departing soldiers, however, Serra startles the men with an accusation. Serra denounces the Spanish military's plans to enslave the "childlike" Indians and plunder their Seven Cities and, pressing a burning torch to his breast, urges the men to behave like "children of God." Before they depart, José complains that Serra carries too many religious "trinkets," but after the expedition is surrounded by armed Indians, the priest prevents an attack by giving the curious visitors strings of colorful beads. When a soldier is killed by an arrow in camp that night, however, José argues that Serra's method of handling Indians is ineffective. Determined to be rid of Serra, Portola feigns concern about an abscess on the priest's leg and orders him back to Mexico City. Serra becomes even more determined to found his missions, and that night, submits to a painful procedure that cures his leg. Later, Serra and José become separated from the column and lose their way in a fierce desert windstorm. Out of nowhere, a shack appears, and they receive food and water from the man, woman and child who live inside. Serra believes they have been miraculously rescued by the Holy Family, but José, an agnostic, is skeptical. The Portola expedition finally arrives at San Diego Bay, only to discover that Rivera's advance party has been decimated by disease. Portola sends the San Antonio back to Mexico City for supplies, places José in charge of the San Diego camp and proceeds northward to Monterey. That night, the Diegueño Indians attack the camp, and Matuwir, grandson of Diegueño chief Miscomi, is wounded. Serra nurses Matuwir back to health and then releases him, thereby infuriating José. Serra soon befriends the villagers, however, and although none of them agrees to be baptized, they begin to visit Serra's Mission San Diego de Alcala regularly. When Miscomi dies, Matuwir is named chief of the Diegueños. Unknown to him and Serra, José pursues and finally makes love to Matuwir's sister Ula. Months later, exhausted and starving, Portola and his men appear, reporting that they were unable to find anything but parched lands and "savages too useless to fight." Because the supply ship has not yet returned from Mexico City, Portola decides to abort the entire California expedition, but Serra persuades him to remain in camp until Saint Joseph's Day. Ula receives Matuwir's permission to accompany José to Mexico City as his wife, but José advises her to remain with her own people. Deeply distressed, Ula runs from José and falls from a cliff to her death. Portola refuses to have José punished "for the benefit of Indians," and Serra refuses to turn him over to the vengeful Matuwir. War drums sound for several days, and the Diegueños sabotage Portola's remaining supply of fresh water. Finally, aware that they will be destroyed by the Indians, Portola orders his men to attack. As Serra blesses them, José confesses his sins and slowly walks out of the camp toward Matuwir's warriors. Serra weeps when José's body, with its heart cut out, is returned to the camp. Because Saint Joseph's Day has dawned without the supply ship having arrived, the expedition abandons the mission and sets out for Mexico City. Shortly after their departure, however, the San Antonio sails into the bay, and the exuberant party returns. As the sailors unload bells meant for the mission at Monterey, Serra rings out a loud, clear tone, "one my Indians will love. I can hear them coming!"