End of the Mission System
After three generations of contact between the Apalachee and Spanish, the Mission and its people appeared very European. Indigenous cultural practices still survived and were practiced, but religious conversion and Spanish customs were heavily enforced. San Luis was truly incorporated into the Spanish Empire.
Due to changes on the international stage the situation could not continue. The English settled Charles Town in present day South Carolina and laid claim to huge portions of Spanish territory. As the empires grew, the Spanish Mission System became a target and St. Augustine was besieged. English raids, supported by their indigenous allies, moved against villages aligned with the Spanish, burning them to the ground and enslaving many of their residents.
The Spanish attempted on multiple occasions to push the English back with Apalachee militia, but were defeated each time. Unwilling to commit to the Spanish cause further due to these losses, noted abuses, and failed promises, the Apalachee chose to abandon San Luis. The Spanish fully acknowledged these failings and, in 1704, worked with the remaining residents to burn the entire Mission to the ground.
With their homes destroyed, the Apalachee people were scattered. Many were enslaved and taken north by the English where they were dispersed and faded away. A small group stayed with the Spanish, taking refuge just outside St. Augustine where over time they succumbed to disease or fully integrated into Spanish society, finally leaving for Havana with the switch to British rule in 1763. The final portion went west, eventually settling in French controlled Mobile, Louisiana. There they survived epidemics and further displacement, and today have descendants who can trace their lineage to those who once lived at Mission San Luis.