Who do the townspeople blame for the epidemic?

The townspeople blame Hannah Tupper for the outbreak of fever in their village.
In chapter 17, a group of people gathers at Matthew Wood's house and demands that he join them in their mission to hunt down Hannah. Matthew, however, refuses to participate in the witch hunt. His refusal angers his neighbors, and one of them warns that his stubbornness will lead to his daughter's death.
The people proclaim that Hannah is a Quaker, an infidel who has been practicing witchcraft for years. However, Matthew refuses to entertain the notion of chasing down an old woman. The people eventually leave, but Kit fears that they will harm Hannah. Her fears prompt her to make her way to Hannah's house. There, she rouses the sleeping Hannah, and the two hide under some brush. 
From there, Hannah and Kit can see the people torching Hannah's house, which eventually burns down. The two then make their way to the river's edge and spend the rest of the night there. In the morning, Kit is relieved when she spots the Dolphin making its way down the river. She swims out to the ship and surprises Nat.
Later, Nat gives Hannah and her cat temporary shelter on the ship.