What's the Name of That Book??? discussion

This kid had an animal sidekick that I think was a bat. I think there was animal experimentation. It was covered up by the town leaders. They had to go in a cave or tunnel in one of the books. Possibly the second book. I think there were potions and plants that had magic properties. I remember very little about this book, so any possible suggestions are welcome!

The Wing and Claw series by Linda Sue Park? The first book is Forest of Wonders.