Though, as we thus see, Father Junipero had ample reason to be encouraged over the progress of his enterprise, he still had various difficulties to contend with. The question of supplies often assumed formidable proportions, and the labors of the missionaries were not always as fruitful as had been hoped. Fortunately, however, the Indians were, as a rule, friendly, notwithstanding the fact that the behaviour of the Spanish soldiers, especially towards their women, occasionally aroused their distrust and resentment. At one establishment only did serious disturbances actually threaten for a time the continuance of the mission and its work. Junipero had lately returned from Mexico, with undiminished zeal and all sorts of fresh designs revolving in his brain, when a courier reached him at San Carlos bringing news of a terrible disaster at San Diego. Important affairs detained him for a time at Monterey, but when at length he was able to get to the scene of the trouble, it was to find that first reports had not been exaggerated. On the night of the 4th of November, 1775, eight hundred Indians had made a ferocious assault upon the mission, fired the buildings, and brutally done to death Father Jayme, one of the two priests in charge. “God be thanked,” Junipero had exclaimed, when the letter containing the dreadful news had been read to him, “now the soil is watered, and the conquest of the Dieguinos will soon be complete!” In the faith that the blood of the martyrs is veritably the seed of the church, he, on reaching San Diego, with his customary energy, set about the task of re-establishing the mission; and the buildings which presently arose from the ruins were a great improvement upon those which had been destroyed.
Before these alarming events at the mother-mission broke in upon his regular work, the president had resolved upon yet another settlement (not included in the still uncompleted plan), for which he had selected a point on the coast some twenty-six leagues north of San Diego, and which was to be dedicated to San Juan Capistrano. A beginning had indeed been made there, not by Junipero in person, but by fathers delegated by him for the purpose; but when news of the murder of Father Jayme reached them, they had hastily buried bells, chasubles and supplies, and hurried south. As soon as ever he felt it wise to leave San Diego Junipero himself now repaired to the abandoned site; and there, on the 1st of November, 1776, the bells were dug up and hung, mass said, and the mission established. It is curious to remember that while the padre-presidente was thus immersed in apostolic labors on the far Pacific coast, on the other side of the North American continent events of a very different character were shaking the whole civilized world.