I've noticed Paizo adventures are chock full of strange coincidences and thematic curiosities. I'll keep track of my observations as I begin playing this...
1) The first encounter features a goat going missing, and a man being blamed for something he didn't do. An ESCAPED GOAT, and a SCAPEGOAT. In Jewish lore, there must be one good goat that is treated well (the goat for Yahweh), and one bad goat that is scorned (the goat for Azazel). This is how a community comes together and purifies itself. In Legacy of Fire, it is how the party comes together and performs its first noble deeds.
3) There is an alchemist's lab in the monastery. Another in Kelmarane, owned by the harpy Undrella. It is stated that she was there when Kelmerane fell.
Was she once a sister of the monastery - a human before she became a harpy? Did she work in the lab, studying the Vardishal mold, and then expand her knowledge by visiting the Shrine of Nethys and beginning work on the Infusium device?
Was she responsible for the plague? Or was she trying to find a cure? Did exposure to the strange magics of the Nethys shrine, or even the wishcraft of the Vardishal mold, transform her into a harpy?
Was it, in fact, Undella, who cured the plague, perhaps by releasing something from the Infusium... but by then she was so far transformed that she could not reveal herself to the people... and by coincidence Xulthos arrived in town and took credit for ending the plague?