'Senyor, pardon, she died, too!'" In 1810 Moraga, the ensign at the presidio, was sent with seventeen men to punish the gentiles of the region of the Carquines Strait, who for several years had been harassing the neophytes at San Francisco, and sixteen of whom they had killed.

Moraga had a hard fight against a hundred and twenty of them, and captured eighteen, whom he soon released, "as they were all sure to die of their wounds." The survivors retreated to their huts and made a desperate resistance, and were so determined not to be captured that, when one hut was set on fire, its inmates preferred to perish in the flames rather than to surrender.

A full report of this affair was sent to the King of Spain and as a result he promoted Moraga and other officers, and increased the pay of some of the soldiers.

He also tendered the thanks of the nation to all the participants.
Runaway neophytes gave considerable trouble for several years, and in 1819 a force was sent from San Francisco to punish these recalcitrants and their allies.

A sharp fight took place near the site of the present Stockton, in which 27 Indians were killed, 20 wounded, and 16 captured, with 49 horses.
The Mission report for 1821-1830 shows a decrease in neophyte population from 1252 to 219, though this was largely caused by the sending of neophytes to the newly founded Missions of San Rafael and San Francisco Solano.
San Francisco was secularized in 1834-1835, with Joaquin Estudillo as comisionado.