WARNING: POSSIBLE SPOILERS
This gives away some stuff, I guess. Not a lot. If you've never seen Doctor Who, GO WATCH IT and come back to this one.
Theory #5
This is by my good friend Whovian_Universe. You should totally follow her. http://w.tt/1kEbEJ9
The Doctor is a human, born in the future and has multiple personality disorder. The second heart was a birth defect, and the "regeneration" process is really the machine that his separate personalities use to remodel his body to their preferences. Being a timelord was a story told to him by his parents to make him feel better about his disorders.
He fought in the war that nearly ended Gallifrey, which was actually colonized by humans, against the Daleks.
The aliens are real, time travel is real, and the Doctor sticks to earth in the past because he is interested of these creatures so close, yet so far to being like him.
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Diving Deeper: A Book of Fan Theories, Easter Eggs and Running Gags
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