Palou eventually established the Mission October 9, 1776.  None of the Indians were present to witness the ceremony, as they had fled, the preceding month, from the attacks of certain of their enemies.  When they returned in December they brought trouble with them.  They stole all in their reach; one party discharged arrows at the corporal of the guard; another insulted a soldier’s wife; and an attempt was made to kill the San Carlos neophyte who had been brought here.  The officers shut up one of these hostiles, whereat a party of his comrades rushed to the rescue, fired their arrows at the Mission, and were only driven back when the soldiers arrived and fired their muskets in the air.  Next day the sergeant went out to make arrests and another struggle ensued, in which one was killed and one wounded.  All now sued for peace, which, with sundry floggings, was granted.  For three months they now kept away from the Mission.

In 1777 they began to return, and on October 4, Padre Serra, on his first visit, was able to say mass in the presence of seventeen adult native converts.  Then, passing over to the presidio on October 10, as he stood gazing on the waters flowing out to the setting sun through the purple walls of the Golden Gate, he exclaimed with a heart too full of thanksgiving to be longer restrained:  “Thanks be to God that now our father St. Francis with the Holy Cross of the Procession of Missions, has reached the last limit of the Californian continent.  To go farther he must have boats.”

In 1782, April 25, the corner-stone of a new church was laid at San Francisco.  Three padres were present, together with the Mission guard and a body of troops from the presidio.  In the Mission records it says:  “There was enclosed in the cavity of said corner-stone the image of our Holy Father St. Francis, some relics in the form of bones of St. Pius and other holy martyrs, five medals of various saints, and a goodly portion of silver coin.”

In 1785 Governor Pages complained to the viceroy, among other things, that the presidio of San Francisco had been deprived of mass for three years, notwithstanding the obligation of the friars to serve as chaplains.  Palou replied that the padres were under no obligation to serve gratuitously, and that they were always ready to attend the soldiers when their other duties allowed.

In November, 1787, Captain Soler, who for a brief time acted as temporary governor and inspector, suggested that the presidio of San Francisco be abandoned and its company transferred to Santa Barbara.  Later, as I have shown elsewhere, a proposition was again made for the abandonment of San Francisco; so it is apparent that Fate herself was protecting it for its future great and wonderful history.

In 1790 San Francisco reported 551 baptisms and 205 deaths, with a present neophyte population of 438.  Large stock had increased to 2000 head and small to 1700.