Combine water and sugar in a small saucepan over medium heat to make simple syrup. Bring to a boil and cook until sugar is dissolved, about 5 minutes. Remove from heat and cool slightly, 7 to 10 minutes.
Combine simple syrup, bacon fat, molasses, and red pepper flakes in a small saucepan. Bring to a gentle boil, stirring frequently, until a thick syrup forms, 10 to 15 minutes. Pour syrup into a freezer-safe container.
Freeze until syrup sets, 1 to 2 hours. Slice into individual caramels and wrap in waxed paper.