In 1798 the padre wrote very discouragingly. The establishment of the villa or town of Brancifort, across the river, was not pleasing. A hundred and thirty-eight neophytes also had deserted, ninety of whom were afterwards brought in by Corporal Mesa. It had long been the intention of the government to found more pueblos or towns, as well as Missions in California, the former for the purpose of properly colonizing the country. Governor Borica made some personal explorations, and of three suggested sites finally chose that just across the river Lorenzo from Santa Cruz. May 12, 1797, certain settlers who had been recruited in Guadalajara arrived in a pitiable condition at Monterey; and soon thereafter they were sent to the new site under the direction of Comisionado Moraga, who was authorized to erect temporary shelters for them. August 12 the superintendent of the formal foundation, Córdoba, had all the surveying accomplished, part of an irrigating canal dug, and temporary houses partially erected. In August, after the viceroy had seen the estimated cost of the establishment, further progress was arrested by want of funds. Before the end of the century everybody concerned had come to the conclusion that the villa of Brancifort was a great blunder,--the "settlers are a scandal to the country by their immorality. They detest their exile, and render no service."
In the meantime the Mission authorities protested vigorously against the new settlement. It was located on the pasture grounds of the Indians; the laws allowed the Missions a league in every direction, and trouble would surely result. But the governor retorted, defending his choice of a site, and claiming that the neophytes were dying off, there were no more pagans to convert, and the neophytes already had more land and raised more grain than they could attend to.
In 1805 Captain Goycoechea recommended that as there were no more gentiles, the neophytes be divided between the Missions of Santa Clara and San Juan, and the missionaries sent to new fields. Of course nothing came of this.
In the decade 1820-1830 population declined rapidly, though in live-stock the Mission about held its own, and in agriculture actually increased. In 1823, however, there was another attempt to suppress it, and this doubtless came from the conflicts between the villa of Brancifort and the Mission. The effort, like the former one, was unsuccessful.
In 1834-1835 Ignacio del Valle acted as comisionado, and put in effect the order of secularization. His valuation of the property was $47,000, exclusive of land and church property, besides $10,000 distributed to the Indians. There were no subsequent distributions, yet the property disappeared, for, in 1839, when Visitador Hartwell went to Santa Cruz, he found only about one-sixth of the live-stock of the inventory of four years before. The neophytes were organized into a pueblo named Figueroa after the governor; but it was a mere organization in name, and the condition of the ex-Mission was no different from that of any of the others.
The statistics for the whole period of the Mission's existence, 1791-1834, are: baptisms, 2466; marriages, 847; deaths, 2035. The largest population was 644 in 1798. The largest number of cattle was 3700 in 1828; horses, 900, in the same year; mules, 92, in 1805; sheep, 8300, in 1826.
In January, 1840, the tower fell, and a number of tiles were carried off, a kind of premonition of the final disaster of 1851, when the walls fell, and treasure seekers completed the work of demolition.
The community of the Mission was completely broken up in 1841-1842, everything being regarded, henceforth, as part of Brancifort. In 1845 the lands, buildings, and fruit trees of the ex-Mission were valued at less than $1000, and only about forty Indians were known to remain. The Mission has now entirely disappeared.