Quote:
Originally Posted by Yamyum
Navi could have flown into the Temple of Time. In Twilight Princess it is shown that the Temple of Time could be accessed by the window. It is a possibility.
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I think that's very likely too. But Link wouldn't have known that the window was only a hologram leading further into the temple. He would have thought it was just a window, so would have looked for her outside in the woods.