In one parallel universe, where Previous Doctor|a version of the Doctor went into hiding on Earth. He commited suicide whilst running away from the timelords persuing him, and in the process regenerated into a female. In this universe it was against the law of the Time Lords to regenerate into a different gender. (AUDIO: Exile)
If you'd like to talk about narrative problems with this story — like plot holes and things that seem to contradict other stories — please go to this episode's discontinuity discussion.