The Mission was founded back in the 1700's by Fr. Serra, who basically walked there from Mexico. Priests were hardcore back then. The Spanish wanted to establish a foothold in the territory before somebody moved in to take it from them, and instead of sending a bunch of soldiers, they sent priests. Turns out this wasn't as cracked as it sounds; the missions those priests founded are still around today. Fr. Serra walked until he got to what would become San Juan Capistrano, met the natives that were living there, the Acjachemen, and set about building the mission and converting them. Within about a generation, the Acjachemen had become the Juanenos, and the Mission at San Juan Capistrano stood in the middle of the wilderness.
There's a graveyard near the back, and everyone buried there, with the exception of Fr. O'Sullivan, is Juaneno. There are thousands of bodies there in a relatively small area; they used to stack bodies vertically in those days.