Due to the mistreatment of the local Yuma Indians, the locals rebelled against Spanish rule, and attacked the mission on November 5, 1775. Father Luis Jayme, who had been left behind to run the mission while Father Serra moved on to found other missions, was killed. Peace eventually settled over the area, and by 1797, there were approximately 1400 Native Americans living in the vicinity of the mission.
After Mexico gained its independence from Spain, it decided that it was not profitable to maintain the missions. The missions were offered for sale to the natives, who were unable to come up with the price, so the mission's property was broken up into ranchos and sold to Mexican citizens. In 1846 the Mission San Diego de Alcalá was given to Santiago Arguello. When the United States took over California, the mission was used by the military from 1846 to 1862. In 1863, President Abraham Lincoln signed an act declaring that all of the 21 missions would become the property of the Catholic Church and have remained so since that time.
When the Mission San Diego de Alcalá was granted back to the Church, it was in ruins. In the 1880s Father Anthony Ubach began to restore the old mission buildings. He died in 1907, however, and the restoration stopped until 1931. In 1941 the mission once again became a parish church. In 1976, Pope Paul VI designated the mission church as a Minor Basilica. The mission is still an active parish serving San Diego.
See also: California mission