Spain sent both military and missionaries to gain control of the new lands of Alta California. Fearing competition from Russia who was establishing settlements north of San Francisco, the Spanish King Carlos III decided to use both. Where a military presence protected vital water 'bays' like the San Diego Bay, using the Catholic Church to development of a mission chain offered a cheaper way to claim the lands. So Spain essentially used missions to solidify their absolute control of Alta California. The Catholic Church saw pagans (native populations) who needed conversion to the Church in order to save their lives. With missions, the priests used baptism (conversion to the faith), and in exchange, forced the neophytes to remain within the mission for necessary education in both religion and trade. The Catholic Fathers wanted to 'civilize' the native populations. It was necessary in order for missions to become self supporting and profitable. I hope this helps explain other issues.
To spread the gospel of Christianity to the indigenous natives.
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