Heh, you think that's freaky...I used to co-write an "Ultimate Batman" fan project? And Thomas Wayne turns out to be Two-Face at the end, a paranoid and superintelligent ganglord. We had it that his marriage was very unhappy, and he orchestrated the assassination in order to traumatise Bruce into an adult mindset while scarring his own face with acid, pretending that it had killed him and thus severing any connection between him and the crime-world.
Martha, however...as an act of mercy, he has the killer aim precisely so that the bullet grazes her, damaging her mental abilities. She spends half a year in a hospital, having lost some of her memory...but when Wayne's henchmen come to check on her one day, they find that she has left, having been checked out by a proven friend of her family. That friend drives her away to a small, sunny town where she used to spend her teens...where she first fell in love, and got her heart broken.