The story gets a tad hard to follow at times, but fro mwhat I've gathered it can be summed up with: Engwithans use animancy to create the gods in order to give people something to believe in and unite them. Thaos spends his entire prolonged life keeping this secret, creating the Leaden Key to make sure no one ever discovers the gods are fake. Since animancy was used to make them, animancers become a threat, so he needs to discredit the whole practice to prevent the secret from being exposed. He does this by siphoning the souls from children and creating an epidemic that they can't solve, using the souls to strengthen Woedica in the process. Eothas notices, marches on Dyrwood, and gets blown up by the Godhammer.
So, wait, why was Thaos working with Woedica? Was it Thaos's plan or hers? What part did she add to it, exactly? How does making her stronger help his cause? Was he working with her from the beginning or only enlisted her help after Eothas things and decided to put a stop to them?
To me, it only makes sense that Woedica got involved after Eothas started marching an army towards the Dyrwood. Thaos needed help, called on her, and her price was giving her the souls he'd been stealing. But if that's the case, why would Eothas create that much of a mess when another god wasn't even involved yet? From what I've gathered, Eothas only did it to put a stop to Woedica's scheme of gaining more power than the rest of the gods. But that means Thaos was working with Woedica for a while. But why would he when he doesn't need her for his plan to succeed?
Create a plague, animancers can't cure it, get blamed, hearings are held, Erl is assassinated by animancers, success is achieved. He doesn't need Woedica for anything except for divine protection from Eothas. Thaos bragged about destroying entire countries to keep his secret and Eothas never intervened before, so why would he now unless Woedica was already working with Thaos?
The plot makes my brain hurt just a bit.