Previously in the story, Nat was banished from Wethersfield under the threat of punishment should he return. Kit is on trial and realizing that the situation is hopeless because, besides her uncle, no one will speak up for her. Just before the end of the inquiry, Nat arrives with Prudence in tow. He has risked his own safety and freedom to help Kit.
The magistrate quizzes Prudence about her ability to read and write. All the while Goodwife Cruff, Prudence’s mother, is railing against Kit as a witch. Prudence is able to show the magistrate that she is able to read and write and explains that Kit taught her. As a result, all charges against Kit are dropped. Nat leaves as soon as it becomes apparent that he has been recognized as a banished person, however the magistrate is willing to let him go since he violated his banishment in order to achieve justice for Kit.
By showing that Prudence can read, he shows that Kit was teaching her to read (and not doing witchcraft). This saves her from a harsh, possibly deadly, punishment.