It's widely believed the island of California was named after a queen in a Spanish novel. Calafia ruled over black Amazons rich in gold, and these rumors fueled the imaginations of Spanish conquistadors. Cortés the Conqueror in 1532 sent a series of expeditions from the Mexican mainland to find this island, making landfall somewhere in Baja near La Paz. These voyages ultimately failed when they discovered, rather than nubile women handing them maps to the gold mines, crowds of equally naked but angry bajacalifornianos with pointy weapons, and the survivors were forced back to the mainland.
In 1539 Cortés sent over Ulloa, who first determined that Baja was a peninsula (although cartographers continued to depict California as a group of islands: Las Californias), naming the "Sea of Cortés" in his patron's honor. Ulloa rounded the peninsula's point in an attempt to find a Northwest Passage to the St. Lawrence, but on the return voyage his ship vanished without a trace, becoming one of those bizarre "Lost Ships of the Desert," legendary vessels that inexplicably began emerging from the sands of the Colorado River around 1870, to believe newspaper accounts of the time.
Cabrillo (who lent his name to yet another colorful San Francisco street), commissioned by the Viceroy of New Spain to find China, cruised by in 1542, and continued up the coast to the Russian River, completely missing what would be San Francisco, as many did owing to the thick blanket of fog hiding the inlet of that pacific bay. Lower California was left to the next wave of conquistadors: pirates.
The turbulent peninsular point became a watering hole for the "Manila galleon" trade ships plying the Acapulco to Manila route beginning in 1565. Spain looked to establish a permanent port, especially after avaricious Dutch and English pirates got wind of the richly laden trade route and began to methodically board and plunder, Sir Francis Drake one of the first of these rowdy buccaneers, adventurers attracted by word of the pearl beds. Woodes Rogers' fleet lay at La Paz to refit with Alexander Selkirk as sailing master, having been rescued the previous year. In desperation, the Spanish crown in Mexico City sent Vizcaíno to stop the ransacking and find a safer port, but about all he did was found La Paz.
Thwarted every step of the way in their efforts to colonize Baja, Spain tried a new approach: sending in the army of God in the form of Jesuit missionaries. The "Pious Fund of the Californias" was amassed with private and churchly contributions. The vice-regal license was given to undertake the conversion of natives, to enlist and pay soldiers, and to appoint or remove officials--on the condition that all be done at the Jesuit's own expense, but that possession be undertaken in the name of the King of Spain.
Jesuits had success in 1697 when in Loreto on the Sea of Cortés they founded the first of the jewels of the California coast--Misión de Nuestra Señora de Loreto Conchó. "Here the inhospitability of Lower California had finally been conquered and a colony had taken root in the face of hunger and mishap," John Steinbeck wrote of Loreto, the first city where Spanish was spoken in California. Hefting the image of the Virgin of Our Lady of Loreto in a sober ceremony, their quest to claim the area for Spain had begun. More Jesuits poured in, eventually establishing a network of 23 missions over the next 70 years.
The strategy for founding missions was first of all to find a site with water, difficult enough in that country "unattractive, indeed repellent, and without elements of riches." Also important was land with good soil and a considerable native population nearby, to give them someone to convert. At first, the Jesuits approached the bajacalifornianos with a peaceful attitude and won their trust with "slight rations of grain and porridge." Later the neophytes resisted control and began to steal, and commit "personal attacks, often repeated, of murderous intent." Along with God and promising pastures, the missionaries brought microbes, and by the end of the Jesuit epoch, the native population was less than 8,000. Although the missionaries forbade fostering the treasure of the pearl fisheries, rumor persisted that the friars were hoarding fortunes and engaging in smuggling.
In 1767, after a series of top-secret meetings in Spain, Kind Carlos III expelled all the Jesuits, sometimes at gunpoint. The king acted upon "urgent, just, and necessary reasons, which I reserve in my royal mind" to suppress the order throughout Spain's colonies. Since the Spanish missions of California were so remote, the decree didn't reach them until much later that year, but by the end of '68, Jesuits were dispossessed throughout Spanish dominions. Instantly the "black robes" of the Jesuits were replaced by the "gray robes" of the Franciscans with their divide and rule policy, and then by Dominicans in 1773.
While the Jesuits limited lay Spanish-Mexican settlement on the peninsula, afraid of corrupting influences and competing power centers, the missions under the Franciscans and Dominicans had to accept a growing lay presence and increased control from central New Spain. Kicking out the Jesuits opened up these territories to settlement and development--such as the founding of Los Angeles in 1781.
The first severe epidemics occurred in 1800-1810. The friars held the belief that epidemics were a punishment from God, so their hands were tied with acquiescence. Why try to alter God's will? Suffering only prepared Indian converts for a superior life in heaven. The mission came to an end in 1829, by which time the native neophyte population throughout Baja California Sur had become extinct.