Over the previous 200+ years of colonial occupation and exploitation of the Americas, The Spanish empire had developed a brutal but effective system for dealing with aboriginal peoples. The mission system was a key component of that system, its job being to turn the natives into Spain's labor force. The paucity of colonists moving from Spain to the New World made that conversion of the indigenes essential if the Spanish Empire was to maintain a hold on its conquests.
The system worked reasonably well in areas of settled, agricultural peoples used to a central government authority. The Aztecs, Mayans, and Incas had authoritarian systems that Spanish conquistadors were able to take over simply by supplanting the native leaders.
In California, the soldiers and missionaries found a very different situation. Small numbers of native peoples lived in small, decentralized tribal arrangements, and the people were unaccustomed to strict authority, regimentation and close-quarters living conditions. When brought into the missions, attrition rates from disease were horrific, and runaways were a constant problem.
At Mission Santa Cruz, Jackson and Castillo document the effects of these twin forces. Within 25 years of the mission's 1791 founding, most of the local natives had either died or run away to areas farther inland. To make up for the lost labor, expeditions were sent far into the interior - as far as the Central Valley - to 1) catch and return runaways, and 2) to compel new tribal groups to relocate to the mission.
The last structure built at Mission Santa Cruz (1820s), and the only one still standing (now the centerpiece of the State Historic Park), was a dormitory for these new arrivals. They had to be kept under guard and separated from the earlier local neophytes, who spoke a different language and were at least partly acclimated to mission life.
The mission system gradually declined until mission secularization dealt the final blow in the 1830s. No longer possessing vast tracts of pasture land, and stripped of authority to requisition native labor, Mission Santa Cruz crumbled away, to be replaced by the Holy Cross parish church we know today. Native neophytes who were supposed to be the eventual beneficiaries of the mission's stewardship were left with very little, and very few fellow natives to share it with.
Things got even worse for native Californians when the 1848 Gold Rush brought tens of thousands of fortune hunters from all over the world to the Sierra foothills. Very few of the newcomers showed much consideration for the people already present, whether Indian or Mexican. Less than two years later, California became the 31st state in the US of A, sealing the fate of native Californians. The second half of the 19th century produced anti-Indian campaigns some have called genocide.
A recent article asks, "On the 140th anniversary of Custer's well-remembered demise, why is California genocide forgotten?" While "genocide" may be too strong a word, it's not far from the truth. Not much more than 200 years ago, the southern and central California coast had the densest indigenous population of any area in all of North America (north of central Mexico).
It's not hard to understand why Californians don't want to talk about the less pleasant parts of the state's history, but we need to be reminded frequently that less-than-noble behaviors are never far below the surface of human nature. There has been social progress in the last 150 years, but we're not out of the cave yet.
