The Portola Expedition, a group of Spanish explorers led by Gaspar de Portolá, laid eyes on the San Francisco Bay a mere 250 years ago. On Nov. 4, 1769 Sergeant Ortega and his men, a subgroup of the expedition, crossed over a hill in what is now Pacifica, beheld the Bay and communicated with Ohlone tribe members in the area. The reality of the Indians would never be the same.
The period up until this point is considered the "Pre-Contact" period. About seven years later, the 8th mission of the mission system was founded: Mission Santa Clara de Asís on the banks of the Guadalupe River in January of 1777, beginning the Mission Era for natives in and around Santa Clara. The Padres made it their goal to ingest as many native individuals into the Mission in order to assimilate them into European culture and convert them to Catholicism. Of course this introduced wide-spread disease and decimated the population, in addition to subverting the Indians' autonomy and sublimating their culture into clandestine practice if not wholly eradicating aspects of it.
It bears mentioning that California Indians from tribes other than the Ohlone and Muwekma Ohlone ended up in Mission Santa Clara, so when we talk about this period of history in context with the Mission, we are talking about a diverse group of Natives.
Mission Santa Clara was not only a church, it was an extensive and complex institution which included housing for the missionaries, the Spanish troops, and the Indians; the kitchen; the cemetery; agricultural fields; grazing lands for the cattle; a corral and slaughter yards; a tannery; a granary; manufacturing sites for textiles and adobe blocks, as well as a threshing floor for the grain. By the 1830s Mission Santa Clara administered 80,000 acres of land, and it also owned thousands of heads of major and minor livestock and produced substantial quantities of various crops.