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The new series, the novels, and the last few seasons of the classic series have occasionally played with the idea—think of the description of who the Pandorica was built for. He occasionally has some darker moments, as seen in "The Family of Blood", "The Waters of Mars", and "A Good Man Goes to War". Additionally, there is a sort of darkness within him, as evidence by the existence of characters like the Valeyard and the Dream Lord. But ultimately, he's on the side of good, and usually his motives and methods are right. It's only because he's a good guy that he's so tortured about the evil he's been forced to do; someone like the Master or Davros doesn't feel the same kind of angst.