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Despite apparent progress and a record baptism of sixty Indians at Mission San Diego in October, 1775, the Spaniards faced a serious uprising. The natives were unhappy about the mission's location at their Nipaguay site and resentful about the intrusion into their lands. On the night of November 5, approximately 600 Indians burned the mission buildings and, during the fire, killed Father Luis Jayme. Two others died and many were wounded but the mission guard prevented further destruction. Plans to attack the presidio failed and fortunately a lack of organization coupled with a fear of reprisal caused the natives to abandon their revolt. Fathers Fermin Francisco cle LaswM, a Spanish Basque, and Gregorio Amurrio from Calahorra were reassigned to aid Vicente Fuster, San Diego's surviving priest, in rebuilding the mission.
These Franciscans first returned to the presidio with their converts and resumed construction of the chapel on the hill. Father Serra conducted a memorial service for the martyred Luis Jayme in Monterey. Governor Rivera and Lt. Colonel Anza toured the local Indian villages seeking to dispel discontent and became satisfied that the uprising had subsided. Father Serra sailed for San Diego on the San Antonio in June and secured the aid of the ship's commander and his sailors in mission construction. The converted Indians, together with the sailors, made adobe bricks, dug trenches, and gathered stone. The new church at the mission was completed in December, 1776.
Anxious about progress in the north, Father Serra left San Diego in the early fall of 1776 and founded Mission San Juan Capistrano on November 1. From there he visited the San Gabriel and San Luis Obispo missions. Fighting heavy winter winds and rain, he journeyed on to San Antonio de Padua and reached Monterey in mid-January 1777. The weary priest rejoiced to find that the presidio and mission at San Francisco (September 17 and October 9, 1776) as well as Mission Santa Clara (January 12, 1777) had been established in his absence.
Father Serra and Governor Rivera were constantly at odds over the founding of new missions. The zealous padre felt that Rivera was overcautious and needlessly opposed to the new settlements. Rivera, on the other hand, wanted to protect his men and the missions with sufficient troops. In mid-1776, Spain reorganized the government of its northern provinces and Monterey succeeded Loreto in Baja California as the seat of the governorship.
Lieutenant Colonel Felipe de Neve, an experienced career officer from Bailen in southern Spain, was appointed governor of both Californias. Rivera returned to Loreto as second in command. Neve traveled overland from Loreto to visit each mission and presidio and to select sites for civilian towns (pueblos). Even though Serra in 1773 had urged that respectable Spanish families be brought into California, he had planned for their settlement around presidios or at the missions under the guidance of priests. Serra believed that pueblos without proper supervision were a questionable improvement and would bring harm to the Indians. Neve, however, planned the founding of San Jose (1777) and Los Angeles (1781) -- towns that were independent of mission jurisdiction.