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My Hero Link
Guardian

Yes, even I have seen draw-backs on this couple, I can see something wrong with any pairing, but it doesn't mean I'm supporting it. This page exists to understand clearly the reasons why Link and Navi aren't/shouldn't be romantically involved.

Link and Navi aren't the same race. Cross-breeding's gross, and besides, Navi is too small to incorporate Link. It's not good on Link's part that he can't even see what Navi looks like, other than a glowing orb with wings.
Like I've stated in 'The Couple', love comes from the heart not form the front of your trousers, and anyway, Hylians and fairies are more magical creatures than us (pathetic) humans. Maybe Link can actually see Navi's face, or has a vision of it. No one said that the fairies of the Legend of Zelda world were humanoid, but still the Great Fairy is.

At the end of Ocarina of Time Navi flies out of the window of the Temple of Time without saying a word.
Goodbyes are always hard, aren't they? In the manga Navi does speak and her lasts words are "Link, I love you". Navi goes back to live in the forest, and since she's not Link's official Kokiri fairy she's not supposed to be with him for those reasons, but if they're good friends then I don't see why not, really. It's not like she said "goodbye", either, so maybe she intended to see him again.

Link loves Zelda because at the end of the game and manga he runs back to the castle to see her, and not anyone else.
He does go back to see Zelda, but at the start of Majora's Mask, if you remember, Link is looking for Navi. He's searching the forest so he can't be looking for Malon etc, and Saria will be in the obvious place of next door to his own home, or in the Sacred Forest Meadow. Besides, it was stated in the manga he was looking for Navi. Plus, the "friend with whom he parted ways when he finally fulfilled his heroic destiny" can only refer to Navi. It could have meant Zelda, but why look for her in the forest? The quote is about his companion - it's clear.