The reasons for Estanislao’s rebellion are not entirely clear, but after escaping the Mission in 1827, by 1828 his raids against the surrounding ranchos and settlements had grown beyond the capacity of the Spanish to tolerate. Two expeditions sent against him, woefully inadequate to challenge Estanislao’s coalition of several thousand Native Americans, met with defeat and loss of life. Finally, a third expedition under Lieutenant Mariano Vallejo (after whom the city of Vallejo is named) joined battle with Estanislao’s forces on the Rio Laquisimas (now known as the Stanislaus River, after Estanislao) on May 19, 1829. After several hours of fighting, Vallejo’s men set fire to the brush surrounding a strongly fortified hill protecting Estanislao’s forces. Combined with artillery fire from Vallejo’s three-pounder cannon, the flames consumed Estanislao’s fortress and flushed his warriors from their positions. A running battle for the next several days broke the Yokut leader’s forces, though Estanislao himself survived to return to the mission and be pardoned later that year. Though he did not give up sporadic raids against the Spanish until 1833, for the last several years of his life he taught the Yokut language to neophytes at Mission San Jose until his death in 1838.
When the newly independent Mexican government seized the missions in 1833, San Jose was the last to be secularized and fared better than most. While others fell into disarray or were abandoned, San Jose survived under government supervision until ownership was returned to the padres in 1843. A mere three years later, however, opportunistic Governor Pio Pico sold the mission for $12,000--an act promptly annulled when the United States annexed California the following year.
San Jose soldiered on until 1868, when a devastating earthquake destroyed the adobe chapel and several other structures. A wooden Gothic Revival chapel was built in its place, which remained until it was moved in 1982 for the reconstruction of the original adobe, completed in 1985. Restoration of the priests’ quarters was accomplished in 1915-1916, and a grove of olive trees planted during Mission San Jose’s early years remains at the site. The present-day chapel is still used for Catholic services. A museum about the Mission’s history occupies the former dormitories, featuring exhibits and artifacts about mission life.