Todd, Viola, and Ben are on the run. After running into the night, Ben gasps for air and makes them take a break. They've reached a cemetery.
Finally—finally—it's time for Ben to let the cat out of the bag. The big secret we've all been waiting for (along with Todd and Viola) is finally exposed: The Noise wasn't caused by the Spackles, but instead existed as soon as the settlers got off the ship. Over time, people grew miserable in their settlements and crops were dying, so they blamed the Spackle and killed them. The men in Prentisstown were still miserable, though, with everyone's thoughts out in the open, so after they killed the Spackle, they killed the women, too. Stay classy, men of Prentisstown.
Jessica Elizabeth (remember Matthew Lyle rambling about Elizabeth?) was the mayor and saw what was about to happen, so she sent some of the younger population away but couldn't get away herself.
Ben didn't leave because he didn't think that the deed would be done, so he's guilty simply because he chose to be ignorant.
This explains why Ben isn't welcome anywhere: The rest of the world has declared Prentisstown criminals and outcasts.
Todd is confused about why Ben and Cillian stayed, but Viola gets it—they protected themselves to take care of baby Todd. And then they protected him from the information about all this stuff, but when he came of age, the mayor was going to tell him.
They hear hoof beats again, and know who it is: Prentiss Jr.
Ben tells Viola and Todd to go and he'll provide a distraction so that they can get away. Todd protests, but Ben points out that he's giving his whole life to keep Todd safe.