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The change to San Rafael had been so beneficial to the sick Indians that Canon Fernandez, Prefect Payeras, and Governor Argüello decided to transfer bodily the Mission of San Francisco from the peninsula to the mainland north of the bay, and make San Rafael dependent upon it.

The citizens subscribed five hundred cattle towards the fund, and Prefect Payeras made an appeal to the various friars which resulted in donations of seven barrels of brandy, worth $575. Before 1821 the walls were raised to the window arches.

The remains of this old Mission of 1802 are still to be seen near Lompoc, and on the hillside above is a deep scar made by the earthquake, this doubtless being the crack described by Padre Payeras. But nothing could daunt the courage or quench the zeal of the missionaries.

In accordance with this order, President Payeras notified Governor Sola of his readiness to give up the Missions, and rejoiced in the opportunity it afforded his co-workers to engage in new spiritual conquests among the heathen. But this was a false alarm. The bishop responded that the decree had not been enforced elsewhere, and as for him the California padres might remain at their posts.

The second shock, a half-hour later, caused the total collapse of nearly all the buildings. Padre Payeras reported that "the earth opened in several places, emitting water and black sand." This calamity was quickly followed by torrents of rain, and the ensuing floods added to the distress of the homeless inhabitants.

In 1823 the Mission lost one of its best friends in the death of Padre Payeras. Had he lived another year it is quite possible his skill in adjusting difficulties might have warded off the outbreak that occurred among the Indians, the famous revolt of 1824. After the attack at Santa Inés the rebels fled to Purísima.

The citizens, however, showed so little interest in the matter that it was not until Payeras made another appeal to his friars that they contributed enough to complete the work. Governor Sola gave a little, and the citizens a trifle. It is interesting to note what the contributions of the friars were.

The Indians of this section were remarkably intelligent as well as diligent, and during the first years of the Mission there were over fifty rancherías in the district. According to the report of Padre Payeras in 1810, they were docile and industrious.

In 1818, when Presidente Payeras visited the Mission, he was not very pleased with the site, and after making a somewhat careful survey of the country around recommended several other sites as preferable.