Ok, this may sound a bit far-fetched, but here goes.
In one of the trailers for Skyward Sword, you see link and his Loftwing flying after a large flying whale. There are tentacles on this whale, with eyes on them, and they are waving about. I think that maybe the whale is the Windfish and instead of being a benevolent deity, he is actually and evil servant of Girahim/Girahim's master. Once you defeat the Windfish in SS the Goddess seals it deep at the bottom of the sea, where it sleeps for hundreds of years guarded by a being called "The Nightmare", until a little boy gets shipwrecked and knocked unconcious. He is technically "asleep" and the Windfish, sencing a power in him, draws the boy into his dream. This boy, Link, gets tricked by the Windfish into thinking he is the good guy and that "The Nightmare" is the bad guy. He does this by using a kind owl that helps him on his journey. When Link get's the the Egg of the Windfish, "The Nightmare" tries to stop him freeing the Windfish by using Links past memories against him, but to no avail. Links "corrupt" mind thinks that he has done good, by vanquishing the evil and freeing the good, but then the Windfish flies free, searching for the goddess so he can get his revenge...
Or in SS the "Windfish" we see is taken over by a monster. Please discuss and notify me of any errors I have accidently put into this post.
In one of the trailers for Skyward Sword, you see link and his Loftwing flying after a large flying whale. There are tentacles on this whale, with eyes on them, and they are waving about. I think that maybe the whale is the Windfish and instead of being a benevolent deity, he is actually and evil servant of Girahim/Girahim's master. Once you defeat the Windfish in SS the Goddess seals it deep at the bottom of the sea, where it sleeps for hundreds of years guarded by a being called "The Nightmare", until a little boy gets shipwrecked and knocked unconcious. He is technically "asleep" and the Windfish, sencing a power in him, draws the boy into his dream. This boy, Link, gets tricked by the Windfish into thinking he is the good guy and that "The Nightmare" is the bad guy. He does this by using a kind owl that helps him on his journey. When Link get's the the Egg of the Windfish, "The Nightmare" tries to stop him freeing the Windfish by using Links past memories against him, but to no avail. Links "corrupt" mind thinks that he has done good, by vanquishing the evil and freeing the good, but then the Windfish flies free, searching for the goddess so he can get his revenge...
Or in SS the "Windfish" we see is taken over by a monster. Please discuss and notify me of any errors I have accidently put into this post.