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My Hero Link
Guardian

The two met at Link's house (ooh, cheeky), when the Great Deku Tree sent Navi to find him. Being in deficit of a fairy all his life, and believe he's suppose to have one, Link got exited about having a fairy in the manga. In the game he sat on the edge of his bed as he listened to her.

 

When they first set eyes on each other

In the game, Link just seems either content or indifferent with Navi because neither of them interact much, nor constantly in full conversation (cor, you wouldn't think of it to look at Navi, would you?). For the sake of the game play and the players, Link is a mute and almost unemotional character who gets on with the quest, while Navi is merely the thing to help you, that's all it is.

I said 'indifferent', but I doubt that's what it is. Link only acknowledges Navi when she's speaking or pointing at something so it's not total ignorance. In the manga, even he gets agitated with her nagging, but they speak and interact more to show it. Link understands Navi is smart about the outside world he knows little about, so he takes her words seriously, yet with a pinch of salt as he acts quickly on it. As depicted by the manga, Navi and Link care about each other's well being.

Sure, Link gets a bit annoyed, and they even fall out in the bonus chapter, but it's normal for two friends too argue. To brings them together and proves they can understand each other. If a pair aren't close enough, why won't have anything to argue about.

 

Navi: No, no! Too many openings! Link: Be quiet, Navi, how can I concentrate? Navi: What? I'm just trying to help!

Navi: Don't be such a sap! Geez! Link: Navi, you're always nagging me! If I'm so bad go follow someone else! Navi: Don't tempt me, Link! I'm only hear because the Great Deku Tree asked me to look after you!

Despite what they say, they made it up in the end, and carried out their relationship which unfolds into a deeper friendship. I'm not trying to make excuses but Navi probably said that last quote because she was angry because she was picked on by Rouru.

 

How happy they were after they realised the need each other