When San Francisco Solano was founded, 92 neophytes were sent there from San Rafael. In spite of this, the population of San Rafael increased until it numbered 1140 in 1828.
In 1824 Kotzebue visited the Mission and spoke enthusiastically of its natural advantages, though he made but brief reference to its improvements. On his way to Sonoma, Duhaut-Cilly did not deem it of sufficient importance to more than mention. Yet it was a position of great importance. Governor Echeandía became alarmed about the activity of the Russians at Fort Ross, and accused them of bad faith, claiming that they enticed neophytes away from San Rafael, etc. The Mexican government, in replying to his fears, urged the foundation of a fort, but nothing was done, owing to the political complications at the time, which made no man's tenure of office certain.
The secularization decree ordered that San Rafael should become a parish of the first class, which class paid its curates $1500, as against $1000 to those of the second class.
In 1837 it was reported that the Indians were not using their liberty well; so, owing to the political troubles at the time, General Vallejo was authorized to collect everything and care for it under a promise to redistribute when conditions were better. In 1840 the Indians insisted upon this promise being kept, and in spite of the governor's opposition Vallejo succeeded in obtaining an order for the distribution of the live-stock.
In 1845 Pico's order, demanding the return within one month of the Indians to the lands of San Rafael or they would be sold, was published, and the inventory taken thereupon showed a value of $17,000 in buildings, lands, and live-stock. In 1846 the sale was made to Antonio Suñol and A.M. Pico for $8000. The purchasers did not obtain possession, and their title was afterwards declared invalid.
In the distribution of the Mission stock Vallejo reserved a small band of horses for the purposes of national defense, and it was this band that was seized by the "Bear Flag" revolutionists at the opening of hostilities between the Americans and Mexicans. This act was followed almost immediately by the joining of the insurgents by Frémont, and the latter's marching to meet the Mexican forces, which were supposed to be at San Rafael. No force, however, was found there, so Frémont took possession of the Mission on June 26, 1846, and remained there for about a week, leaving there to chase up Torre, who had gone to join Castro. When he finally left the region he took with him a number of cattle and horses, went to Sonoma, and on the 5th of July assumed active command of all the insurgent forces, which ultimated in the conquest of the State.
From this time the ex-Mission had no history. The buildings doubtless suffered much from Frémont's occupancy, and never being very elaborate, easily fell a prey to the elements.
There is not a remnant of them now left, and the site is occupied by a modern, hideous, wooden building, used as an armory.