Governor Sola and Padre RamÛn Abella at mission San Francisco de Asis were very concerned about high death and sickness rate among the soldiers, settlers but most devastatingly among the Native Americans. Governor Sola suggested an experiment: to move the ill to a sunnier site, the expedition group included: a group of Padres including Padre Gil y Taboada and Padre Vicente de Sarria. After a short time, the experiment seemed to be working and the patients showed improvement, and that ís how this mission came to be!

The area had much better weather and was protected from clouds and rain by hills. After completion of a small building in San Rafael, sick neophytes (Christian Native Americans) from Asis mission were transported, wrapped in blankets and rowed across the bay. Soon, there was a remarkable improvement. Word of this spread and other missions began sending sick to the San Rafael Archangel mission.

A year after the mission hospital was built; simple adobe buildings were added at the site. The main building was 87 feet long and 42 feet wide. It was basically all one building, divided into the storehouses, a hospital and a monastery. A church was constructed too at one end of the building, 90 degrees to the main building. It had no bell tower but four small bells were hung on a simple frame.

Two years later Padre Juan Amoros from Carmel replaced Padre Gil. In 1842, the hospital became a real mission. General John C Fremont was at San Rafael Archangel when his lookouts spied three people land from a boat that crossed from. Kit Carson was one of those men sent to intercept them. Carson asked Fremont if they were to be captured. Fremont replied "I have no room for prisoners." With those words in mind Carson's party approached them and shot them. Sadly the men were from the area where Fremont had recently stayed. Some believed they were messengers but we will never know.

Under Padre Amoros' control San Rafael flourished even more. So, on this date the Asistencia was promoted at the Mission status. Production at the mission continued to increase and it became famous for its pears. When Padre Amoros died this year. Padre Jose Maria Mercado replaced him. Unfortunately Padre Mercado was short tempered and often acted rashly. Reports are that Padre Mercado saw a group of Native Americans he did not recognize approaching, he armed a group of Neophytes and ordered them to attack, His band killed 21 Native Americans and wounded many. For that he was suspended from the mission for six months. Eventually the mission was abandoned and torn down, after a few years a replica of it and the church was rebuilt.