In 1774, the separation of the Mission from the presidio was decided upon, in order to remove the neophytes from the evil influences of the soldiers. The site chosen was six miles up the valley (named Nipaguay by the Indians), and so well did all work together that by the end of the year a dwelling, a storehouse, a smithy built of adobes, and a wooden church eighteen by fifty-seven feet, and roofed with tiles, were completed. Already the work of the padres had accomplished much. Seventy-six neophytes rejoiced their religious hearts, and the herds had increased to 40 cattle, 64 sheep, 55 goats, 19 hogs, 2 jacks, 2 burros, 17 mares, 3 foals, 9 horses, 22 mules,—233 animals in all.
The presidio remained at Cosoy (now old San Diego), and four thousand adobes that had been made for the Mission buildings were turned over to the military. A rude stockade was erected, with two bronze cannon, one mounted towards the harbor, the other towards the Indian rancheria.
The experiments in grain raising at first were not successful. The seed was sown in the river bottom and the crop was destroyed by the unexpected rising of the river. The following year it was sown so far from water that it died from drought. In the fall of 1775 all seemed to be bright with hope. New buildings had been erected, a well dug, and more land made ready for sowing. The Indians were showing greater willingness to submit themselves to the priests, when a conflict occurred that revealed to the padres what they might have to contend with in their future efforts towards the Christianizing of the natives. The day before the feast of St. Francis (October 4, 1775), Padres Jayme and Fuster were made happy by being required to baptize sixty new converts. Yet a few days later they were saddened by the fact that two of these newly baptized fled from the Mission and escaped to the mountains, there to stir up enmity and revolt. For nearly a month they moved about, fanning the fires of hatred against the “long gowns,” until on the night of November 4 (1775) nearly eight hundred naked savages, after dusk, stealthily advanced and surrounded the Mission, where the inmates slept unguarded, so certain were they of their security. Part of the force went on to the presidio, where, in the absence of the commander, the laxity of discipline was such that no sentinel was on guard.
An hour after midnight the whole of the Mission was surrounded. The quarters of the Christianized Indians were invaded, and they were threatened with instantaneous death if they gave the alarm. The church was broken into, and all the vestments and sacred vessels stolen. Then the buildings were fired. Not until then did the inmates know of their danger. Imagine their horror, to wake up and find the building on fire and themselves surrounded by what, in their dazed condition, seemed countless hordes of savages, all howling, yelling, brandishing war-clubs, firing their arrows,—the scene made doubly fearful by the red glare of the flames.