King Carlos III of Spain became very concerned about the possibility of other world powers such as Russia, England, France and Prussia threatening Spanish territories in America. He thought the best way of protecting and expanding his control of this region was to dispatch additional missionaries and colonizers.
Since the beginning of the century, Jesuits had been working in the Americas. Don Denevi argues: "For seventy years, more than six hundred Jesuits had toiled in Baja California, steadily moving northward, evangelizing everyone in their path, never abandoning a mission. With patience and devoted zeal, they had accomplished what Cortes had been unable to do with the sword - Spanish domination over the native populations."
Carlos III questioned the loyalty of these Jesuits to the Spanish monarchy. On 27th February, 1767, Carlos III issued a royal decree known as the Pragmatic Penalty of 1767, that led to the Jesuits being expelled from Spain. All their possessions were also confiscated. The king also wanted the Jesuits removed from territories he controlled in the Americas. He wrote to Carlos Francisco de Croix, viceroy of New Spain, on 24th June, 1767: "Repair with an armed force to the houses of the Jesuits. Seize the persons of all of them and within twenty-four hours transport them as prisoners to the port of Vera Cruz... If after the embarkation there should be found one Jesuit in that district, even if ill or dying, you should suffer the penalty of death."
Gaspar de Portolà was appointed as governor of Baja California with orders to expel the Jesuits from the territory. When the Jesuits rebelled against this persecution, he dealt severely with the rebels, hanging the leaders. The viceroy defended his actions by claiming that: "It is done... for motives known to the royal conscience of the sovereign, and which have to be acknowledged by the vassals of His Majesty, who have been born to obey and not to mix in the high affairs of government."
Carlos Francisco de Croix suggested to Carlos III that the Franciscans should attend to the people of Baja California. It was also agreed that the missionaries should push on quickly into Alta California in order to build a chain of missions that would stop other countries to try and colonise this territory. When asked to organise this campaign, the College of San Fernando de Mexico unanimously selected Junipero Serra, to carry out this task. Serra became president of these missions and Francisco Palóu was appointed as his deputy. As a result of these developments, Francisco Garcés was assigned to Mission San Xavier del Bac near present-day Tucson.
Viceroy Antonio María de Bucareli asked Juan Bautista de Anza to explore the land north of New Spain. He decided to take Francisco Garcés with him. On 8th January, 1774, Anza and Garcés left Tubac with 34 soldiers. Kevin Starr, the author of California (2005) has argued: "Captain Anza - a longtime veteran of frontier service with an outstanding reputation - set forth from the presido at Tubac, south of the present-day city of Tucson, with thirty-four soldiers and one Franciscan, Francisco Garcés, himself an experienced explorer." Anza reached Mission San Gabriel on 22nd March, 1774. He then marched north to Monterey before returning to Tubac. As Starr has pointed out: "In one heroic trek, Anza had linked California overland to northern New Spain."
The Spanish Government was eager to establish an overland link between California and New Spain and needed to establish a presence to protect point where travelers would ford the Colorado River. In January, 1781, Father Francisco Garcés, with the support of Juan Bautista de Anza, established the Mission San Pedro y San Pablo de Bicuñer. However, unlike the missions established by Junipero Serra, the powers of administration rested with the military and not with the padres, as a result the soldiers were abusive to the local Native Americans. Spanish colonists were also accused of seizing the best lands in the area. This caused conflict with the Native Americans.
In the summer of 1781, Fernando Rivera Moncada and a small group of soldiers advanced across the desert with a vast herd of animals, estimated to nearly 1,000 in number. On 17th July, while camped on the banks of the Colorado near Yuma, Rivera and his men were killed by a surprise attack by the Quechan tribe. They then went on to kill Francisco Garcés and the other missionaries at the Mission San Pedro y San Pablo de Bicuñer. The mission was never re-established and the overland route to Alta California was considered too hostile to be used and was therefore abandoned.