In that first decade two missions were founded in the Bay Area at San Francisco (1776) and Santa Clara (1777) and hundreds of Indians went to live at the Missions while others worked as day laborers. Once indians were baptized, the missionaries kept close track of them, expected them to turn away from their old traditions, and used soldiers and the threat of force to keep order.
The Native Americans came to the missions for a variety of reasons. Many wanted to ally themselves with the powerful newcomers and thus have an advantage over other Indian tribes. Eventually their food supplies were damaged by the Spanish grazing and cultivation practices. Foreign diseases for which they lacked immunity decimated them. The physical, social and psychological environments of their tribes deteriorated and village life collapsed.
Tatcan Indians, probably from the Alamo and Danville area, went to Mission Dolores in San Francisco early in 1795 along with a large contingent of Lafayette area Saclans. A devastating epidemic (perhaps typhus) killed many of them in March and April. Soon after, Saclans (from Lafayette) and others left the Mission in large numbers, becoming part of a major organized Indian resistance in the East Bay. Because of this hostility Mission San Jose was located only 13 miles from Mission Santa Clara, instead of in the San Ramon or Amador Valleys.
Indians from the eastern valleys began to come to Mission San Jose after it was founded in 1797, although in the early years unfriendly Indians threatened anyone who went there. By 1806 there were 662 Indians at the Mission, with a peak population of 1,886 in 1831. Most Tatcan Indians, who spoke Bay Miwok and lived along San Ramon Creek, went to Mission Dolores from 1795 to 1806. The Ohlone (Costanoan) Indians, including Seunen from the south San Ramon and Dougherty Valley areas, are recorded as having arrived at Mission San Jose beginning in 1797. In 1805 some Seunens joined with Volvons to plot against Mission Santa Clara, but a large Spanish expedition squelched their plans.