Kino died in 1711 and it is uncertain how much of the building had been completed. In 1751 the generally peaceful Pimas, disturbed by the inroads being made by Spanish settlers and prospectors, revolted and plundered the mission. Some of the Indians had been obliged to work in the mines, practically as slaves for the Spanish colonists, and it is probable that others found the discipline and regular work of the padres burdensome. All Pimería was shaken by this great uprising which nearly wiped out the frontier missions. The following year a presidio was established at the visita of Tubac, 37 miles to the south, for the protection of San Xavier, its visitas, and the villages of the Christian Indians. Missionary activities were again started and many of the Indians who had previously fled, returned. In 1767, by Royal Order, the Jesuits were expelled from all Spanish domain. Charles III of Spain, fearing the Jesuits were too persistent in their quest of new lands, decided to replace them with the Franciscan Order. San Xavier, like most of the abandoned missions of the region, was taken over by the Franciscans in 1768. San Xavier came under the direction of Friar Francisco Garcés and before the year was out, while he lay sick at a nearby visita, the mission buildings were destroyed by Apaches. The padres’ courage and spirit were unshaken however, as we find that four years later a “fairly large” church was erected. The danger from Apache raids became increasingly serious and in 1776, a presidio was established at nearby Tucson for greater protection of San Xavier. About 1785 two Franciscan friars, successors to Garcés, began work on the building. This evidently was at the site of the present mission. What part, if any, of the present structure belongs to the period of Jesuit occupation is conjectural and there seems to be some confusion at this period regarding the two sites. However, the cruciform (cross-shaped) design of the present structure was not used by the Franciscans for missions and it is reasonable to suppose that the Jesuits may have laid the foundations for the present church, under these circumstances. Also, the name of San Xavier, a Jesuit, was retained, while the Franciscans changed the names of the other Jesuit missions. The labor of building went on for more than ten years. Except for part of one tower, the structure was probably finished in 1797, as an inscription on the door of the Sacristy indicates: “Pedro Bojs ano die—1797 (Pedro Bojourques—on a day in the year 1797).” The actual building of San Xavier was carried on under the direction of Ignacio Gaona, Spanish architect and master mission builder. Ornaments and fixtures of the older church were placed in the new building.