How to explain the powerful and in many respects unique religiosity encountered by Pope Francis on his trip to Mexico last week? Its roots are deep in history.

The conquistador Hernán Cortés explored and conquered Mexico in the early 16th century, but even before his death the Spanish state and the Catholic Church had taken dominion over the lands the conquistadors discovered, giving the Mexicans no choice but to embrace the faith. As the indigenous peoples converted, however, their churches took on a distinctive character.

After the fall of Tenochtitlan, the Aztecs’ capital, they assumed the role of a defeated people. More thoroughly than the tribes that had not previously formed part of their empire, they were immediately enslaved. Their first task was to clear the rubble of their destroyed capital and then, using the stones from their temples and pyramids, to build the churches and palaces of their new masters.

The architects were Spanish, but the craftsmen were Indian and their skills and tastes added to the ornateness of the stone carvings covering the new edifices. From the early sixteenth century, in fact, a new mestizo style—Mexican Colonial—was born, combining the baroque and the Aztec, creating magnificent buildings that seemed to capture the deep melancholy of the conquered race.

In “urban” areas, the Indians resigned themselves to their fate, recognizing their defeat as the defeat of their gods and therefore gradually transferring their loyalty to the god of the Spaniards. Catholic missionaries in turn accepted a blending of Christianity with the religious traditions of the Indians. The concept of building churches on or near the sites of temples enabled the Indians to continue their pilgrimages. And by no small chance, it was close to the sanctuary of the goddess Tonantzin on the Hill of Tepeyac outside Mexico City that the “dark” Virgin of Guadalupe first appeared to a humble Indian, Juan Diego, on December 12, 1531.

Religious syncretism thus took place easily: not only did the profusion of Catholic saints match the myriad pre-Hispanic gods, but both religions included much pomp and ceremony and sustained precepts of punishment and reward which made even the Inquisition understandable.

As the conquistadors struck out from Mexico City to “tame” the indigenous people, they spread death, not only through destruction and massacres but also through European diseases that took the lives of perhaps two-thirds of Mexico’s Indians during the sixteenth century alone.

Missionaries followed—first Franciscans and later Dominicans, Augustines and Jesuits—and in their effort to repair the damage caused by the conquistadors, they left a trail of churches, convents and schools in their path. Through the campaigning of one priest, Bartolomé de Las Casas, the Council of the Indies freed all Indians from slavery in 1542.

The Indians were still regarded as minors who required spiritual education, but the new practice of placing them under the guardianship, or encomiendas, of landowners was also banned by Spain, which preferred that they depend directly on the Crown than on new fiefdoms. Some Indians successfully retreated into mountains, jungles and deserts— to lands that the conquistadors had little interest in exploiting. But most could only withdraw into their souls: already, pride and tradition sought to live on behind a mask of subservience and formality.

Four centuries later, as Mexico underwent a series of revolutions and saw the rise of new caudillos, or dictators, many of the poor turned their anger against the Church identified with the rich and with their continued serfdom. And some of the strongmen who emerged launched relentless attacks on the clergy.

President Plutarco Elías Calles, in the 1920s and 1930s, was especially ruthless in his persecution of the Church. The traditional anticlericalism of the Mexican Liberal Party had been reinforced by the Church’s support for previous dictatorships. Still more crucial, the post-revolutionary regime viewed the Church as a permanent obstacle to consolidation of its power and modernization of the country.

The 1917 Constitution had nationalized churches, established that only Mexican nationals could be priests, banned religious processions and forbade clergy from appearing in public in cassocks, from voting or discussing politics, from owning property and from involvement in education. But it was only under Calles that these articles were strictly enforced.

When the government required additionally that all native-born priests be licensed in 1926, the Catholic hierarchy ordered a boycott of churches by the clergy. In the western states of Jalisco, Michoacán, Guanajuato, Colima and Zacatecas, fanaticized peasants led by conservative priests then launched a guerrilla war to the cry of "Viva Cristo Rey!"—“Long live Christ the King!”—which gained them the name Cristeros. And in the name of Christ, they carried out murder, arson and sabotage.

The government promptly responded in kind, unleashing a fierce wave of persecution throughout the provinces. Cristeros were massacred and priests hanged, while in other regions masses were held in secret.

In the southeastern state of Tabasco, Governor Tomás Garrido Canabal organized bands of “red shirts” to attack priests and destroy churches. In Mexico City, it became fashionable to loot churches of their Colonial art. Even after 1929, when the dispute was formally settled and churches reopened, religious fanaticism and confrontations persisted. In 1932, the archbishop of Morelia was deported amid official warnings that renewed agitation would lead “churches to be turned into schools and workshops for the benefit of the proletariat.”

In 1935, there were still bloody clashes in Mexico City between Catholics and “red shirts.” In the late 1930s, a new ultraconservative religious movement called Sinarquismo emerged among the peasants of the Bajío region. But the traditional power of the Catholic hierarchy had been broken. The removal of the Church from politics consolidated the revolutionary leadership and centralized bureaucracy that had come to power a decade earlier.

Excerpted from Distant Neighbors by Alan Riding. Copyright © 1984, 1989, 2000 by Alan Riding. Reprinted by permission of Alfred A. Knopf/Vintage Books, an imprint of the Knopf Doubleday Publishing Group, a division of Penguin Random House LLC. All rights reserved.