There could be a lot of oppurtunities for this change...these are some of the things I can think of..
Link finds out about his sister, so he decides to see her, and Ganon kidnaps her.
A new foe kidnaps Link's sister and he has to save her.
Link's sister is the main bad ass of the game because she is possessed or evil has overtaken her and Link has to save her.
Link's sister is a magical goddess that wears speedos.
And so on..
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