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Innocent realized that the king benefited most from this new arrangement. But Spain was a bastion of Roman Catholicism, and the pope knew that Spanish exploration gave him the opportunity to spread the faith in previously unknown regions. Church and state would colonize the New World together, and each would help the other. By evangelizing the Indians and familiarizing them with Spanish culture, the missionaries would prepare them for citizenship and loyalty to the new state. And the crown, by providing peace and stability in the land, would make such proselytizing possible.

What method would they use to accomplish these goals? The Spanish crown first tried to civilize the indigenous peoples of the New World with the encomienda, a system that granted a Spanish colonist "charge" or "responsibility" over a group of Indians in return for his services to the crown. Yet it soon became apparent to missionaries such as Bartolome de las Casas that colonists were abusing the system. In 1573, the crown replaced the encomienda with the reduccion, a mission compound separated from Spanish colonial society and protected by a nearby fort, or presidio, in which soldiers from the army were housed. Under this new system, missionaries could then instruct their converts as they wished without much outside interference—that is, until they felt that the natives were ready to enter Spanish society.

This was the context for the California missions—a task taken up by the Franciscan "religious" order, since "secular" bishops were charged with caring only for their own flocks, not pioneering new ones. By the 1630s, the Franciscans had built a thriving community of 50,000 converted Indians in New Mexico. They exercised remarkable control over their own affairs, drawing only on the services of a nearby presidio when military protection was needed. Now the friars were poised to expand their work along the Pacific seaboard.

Events in Spain were to change all this, however. The Bourbons, a family originally from France, took control of the throne at the beginning of the 18th century, and they brought a "progressive" agenda along with them. Philip V set out to revitalize the economy, passing laws favorable to commerce, business and competition. He also brought a high degree of centralization to the government, implementing a series of reforms designed to increase government efficiency. In addition, Philip decided it was time for the court to intervene more directly in the affairs of the church.

The missionary enterprise in California, then, was one dogged by increasing governmental interference. As the Spanish court became more "progressive" under the influence of the Enlightenment, it saw the patronato real less as a partnership and more as an opportunity to subjugate the church to the aims of the crown. Junipero Serra, father and presidente of the missions, clashed with every governor appointed to California. Pedro Fages, commander of the military in California from 1770 to 1774, insisted on having the authority to choose which soldiers protected the missions, arguing that all civil and military power belonged to him alone. Serra resented this intrusion, as he wanted to hand pick the men who interacted with Indian converts. He feared (with good reason!) the immoral designs some of the soldiers had on Indian women. At the mission of San Gabriel, Spanish soldiers once lassoed and raped some women, in one case killing a native husband who was attempting to protect his wife. The women, in turn, protested by aborting children conceived by these violations.

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