The missionaries experienced immense setbacks in 1690, however. A smallpox epidemic broke out within the area and took the lives of around 300 individuals in the vicinity of the mission and another 3,000 in the outlying area. The natives blamed the Spaniards for the disease, thinking that it was caused by the Holy Water of Baptism. According to the Interpretive Guide to Mission Tejas Stat Park, Adding to growing
hostilities, Casañas challenged the established Nabedache religious
leaders, ridiculed their sacred items and practices, and earned powerful enemies. For the next 40 years, the friars, soldiers and settlers
attempted to maintain a successful community.
In 1962, after experiencing long periods of drought, the tensions between the Spaniards and the Nebedache were running extremely high. In 1963, Father Massanet was tipped off that the Nebedache were planning to attack the Spaniards, and so, [w]ithin
two weeks the Spaniards loaded supplies, buried heavy items, and
burned Mission Tejas. Under cover of darkness the Spaniards
began their retreat to Monclova, Mexico.