Mission San Diego de Alcalá, also known as the San Diego Mission Church, was founded on July 16, 1769, the first in the twenty-one Alta California mission chain established by Father Presidente Junípero Serra; today it is known as "California's First Church." Spanish explorer Sebastián Vizcaíno named San Diego Bay San Diego de Alcalá when he made landfall there in 1602, some ten miles from the present Mission site. In 1773 the Mission was the site of the first Christian burial in Alta California; San Diego is also generally regarded as the site of the region's first public execution in 1778. Father Luís Jayme, "California's First Christian Martyr," lies entombed beneath the chancel floor. The current church is the fourth to stand on this location. The Mission is a National Historic Landmark.
The former Spanish settlement at Nipawai lies within that area occupied during the late Paleoindian period and continuing on into the present day by the Native American society commonly known as the Diegueño; the name denotes those people who were ministered by the padres at Mission San Diego de Alcalá. Relatively much is known about the native inhabitants in recent centuries, thanks in part to the efforts of the Spanish explorer Juan Rodríguez Cabrillo, who documented his observations of life in the coastal villages he encountered along the Southern California coast in October of 1542. Cabrillo, a Portuguese navigator in the service of Spain, is credited with the "discovery" of San Diego Bay. On the evening of September 28, 1542 the ships San Salvador and Victoria sailed into the harbor, whereupon Cabrillo christened it "San Miguel. During that expedition a landing party went ashore and briefly interacted with a small group of natives. Some sixty years later another Spanish explorer, Sebastián Vizcaíno, made landfall some ten miles from the present Mission site. Under Vizcaíno's command the San Diego, Santo Tomás, and frigate Tres Reyes dropped anchor on November 10, 1602, and the port was renamed "San Diego de Alcalá.
It would be another 167 years before the Spanish returned to San Diego. Ever since the voyages of Christopher Columbus, the Kingdom of Spain sought to establish missions to convert the pagans in Nueva España ("New Spain") to Roman Catholicism in order to facilitate colonization of these lands. However, it was not until 1741—the time of the Vitus Bering expedition, when the territorial ambitions of Tsarist Russia towards North America became known—that King Philip V felt such installations were necessary in Upper California. Finally in 1769 Visitador General José de Gálvez sent the expedition of Junípero Serra and Gaspar de Portolà to found a mission at San Diego and presidio at Monterey, respectively, thereby securing Spain's claim to the entire Pacific Coast by right of discovery. Two groups traveled from Lower California on foot, while a pair of packet ships (bearing supplies) traveled up the coast from the Baja Peninsula.
The first expedition to reach San Diego came by sea aboard the packet ship San Antonio, commanded by Captain Juan Pérez, which sailed into port on April 11 and dropped anchor near Point Guijarros. Under the command of Captain Vicente Vila, the San Carlos (formerly the Golden Fleece), despite having put to sea well ahead of her sister ship, nonetheless did not arrive in San Diego until the afternoon of April 29, severe storms having hampered her progress. The first overland expedition, under Captain Fernando Rivera y Moncada, completed their journey on the afternoon of May 4, while Governor Portolà's contingent arrived on June 29. Many members of the overland expeditions fell ill along the way, and a majority of the crews from both ships contracted scurvy during their voyages; in all, over a hundred men (including the crew of a third ship, the San José which went down enroute) died. Portolà and the "Sacred Expedition" continued on to Monterey Bay on July 14, and just two days later, on July 16, a cross was raised and Father Serra held the first Holy Mass; Mission San Diego de Alcalá was officially founded. The padres' initial efforts to establish an outpost at the San Diego met with little success. The Mission was founded at a site overlooking the Bay known today as "Presidio Hill" (Kosoi to the natives), but the natives resented the Spaniards' intrusion, and the settlement was attacked within a month. By the first few months of 1770, food had run low, no permanent buildings were erected, and there had yet to be a single conversion. Four soldiers, eight Catalonian volunteers, one servant, and six Christian Indians from Lower California had died from scurvy since the expedition's arrival; serious consideration was therefore given to abandoning the site and returning to the Baja settlements. It was therefore determined that, if a supply ship did not arrive by March 19 (Saint Joseph's Day), the expedition would be recalled. Father-Presidente Serra, in response, wrote a lengthy letter addressed to Father Francisco Palóu the following day:
Four Fathers, Fr. Juan Crespí, Fr. Fernando Parrón, Fr. Francisco Gómez, and I, are here, ready to found a second mission, if the ships arrive. Should we see that hope and supplies are vanishing, I shall remain here alone with Fr. Juan Crespí and hold out to the very last. May God give us His holy grace. Recommend us to God that so it may be...
Serra feared that if San Diego were abandoned, "..centuries might come and go before the country would again be revisited...;"finally, just before sunset on the 19th, the San Antonio entered the harbor. The ship had been bound for Monterey to deliver supplies to the expedition waiting there, but had lost one of its anchors and was forced to make port in San Diego, where a spare anchor from the San Carlos could be retrieved. With the settlement now properly putfitted with supplies, the missionaries set about constructing permanent buildings at Kosoi, in 1773 the site of California's first Christian burial. The Mission was relocated to its present location (the native village of Nipawai) in August of 1774. The lack of a dependable water supply, coupled with the proximity of the military personnel at the presidio, led Father Luís Jayme to seek permission to relocate the mission from its original site, to the valley some six miles upriver to the east, where it remains today. Almost immediately there was a noticeable increase in the number of baptisms, which in 1775 totaled 431 (compared to 274 for the preceding four years combined).
Native resistance continued almost unabated. At approximately 1:30 a.m., on the moonlit night of November 4, 1775 between 600 and 800 warriors from the surrounding rancherías silently crept into the mission compound. After plundering the chapel, they set the other buildings ablaze. The commotion soon awakened the two missionaries, the Spanish guards, and the Christian neophytes. Fray Jayme (who had been left behind to run the Mission while Father Serra moved on to found other missions) was killed in the melee, thereby making him California's first Christian martyr. The Mission buildings were reduced to ashes, and all records and manuscripts lost in the blaze; the censer, the chalice used at Holy mass, and the pieces of coin used during marriage ceremonies were "melted into a solid mass. The following February, one of the neophytes who had participated in the assault repented and sought refuge in the jacal then being used for Divine service. Captain Rivera refused to recognize the native's claim of sanctuary, reasoning that "...the [place] where Holy mass was celebrated was not a church but a warehouse. Though threatened with excommunication, Rivera remained determined to remove the Indian (by force if necessary) and did so personally on March 26, 1776. Seeking to have his excommunication lifted, he traveled to Monterey to bring the matter directly before Father Presidente Serra. After hearing the captain's arguments and reviewing several letters sent by the Mission fathers regarding the incident, Serra decided that Rivera was to return the prisoner to the church in San Diego, and that Fathers Font and Fustér would thereupon lift the excommunication.
San Diego achieved the reputation early on as site of the region's first public execution, one it may not deserve. On April 6, 1778 four native chiefs of Pámo, one of San Diego's Indian rancherías, were convicted of conspiring to kill Christians and were sentenced to death by José Francisco Ortega, Commandant of the Presidio of San Diego; the four were to be shot on April 11. However, there is some doubt as to whether or not the executions actually took place.
José María de Echeandía, the first native Mexican to be elected Governor of Alta California, issued his "Proclamation of Emancipation" (or "Prevenciónes de Emancipacion") on July 25, 1826. All Indians within the military districts of San Diego, Santa Barbara, and Monterey who were found qualified were freed from missionary rule and made eligible to become Mexican citizens; those who wished to remain under mission tutelage were exempted from most forms of corporal punishment. Catholic historian Zephyrin Engelhardt referred to Echeandía as "...an avowed enemy of the religious orders." Although Governor José Figueroa (who took office in 1833) initially attempted to keep the mission system intact, the Mexican Congress nevertheless passed An Act for the Secularization of the Missions of California on August 17, 1833. The Act also provided for the colonization of both Alta and Baja California, the expenses of this latter move to be borne by the proceeds gained from the sale of the mission property to private interests.
The goal of the missions was, above all, to become self-sufficient in relatively short order. Farming, therefore, was the most important industry of any mission. Prior to the establishment of the missions, the native peoples knew only how to utilize bone, seashells, stone, and wood for building, tool making, weapons, and so forth. The missionaries discovered that the Indians, who regarded labor as degrading to the masculine sex, had to be taught industry in order to learn how to be self-supportive. The result was the establishment of a great manual training school that comprised agriculture, the mechanical arts, and the raising and care of livestock. Everything consumed and otherwise utilized by the natives was produced at the missions under the supervision of the padres; thus, the neophytes not only supported themselves, but after 1811 sustained the entire military and civil government of California. Wheat, corn, wine grapes, barley, beans, cattle, horses, and sheep were the major crops at San Diego. In 1795, construction on a system of aqueducts was begun to bring water to the fields and the Mission (the first irrigation project in Upper California). The building manager was Fray Pedro Panto, who was poisoned by his Indian cook Nazario before the project was completed.