This is my first post! My name is Erik and I have been a Zelda fan since I was very little. It has been my favorite series since.
Today, I finally got around to beating Master Quest, and for the first time the ending really caught me off guard.
Navi just leaves Link without saying a word, no goodbye at all, after the adventure they just completed together. I really sensed a close friendship when Navi came back to Link's side fighting Ganon after she was unable to assist him against Ganondorf due to the dark magic.
It really seemed like she was happy to be helping him in that scenario, and that she cared about Link.
At the end, she leaves and presumably goes back to the Kokiri Forest without saying a word or even looking back to Link.
I think that she leaves in order to fulfill her destiny. I think that there really was no more use for her, and her knowledge may have been limited to the information needed to complete missions within OoT.
Maybe she didn't have a choice in the matter? Maybe her presence tripped something and she got summoned away. Of course, that still wouldn't explain why the Hero of Time didn't just wait for the Deku Tree Sprout to show up and ask it to summon her back.
You know, I was thinking about this when I though: Maybe the goddesses possessed navi and made her leave, so that link would go out and look for her, and thus leading to the events of MM. Meaning the Goddesses wanted link to save Termina.
I don't want to phrase it this way because all the Navi haters would rejoice, but I'm starting to think for some reason she went off and ended her life (maybe of old age, maybe not). Think about this: She had great, great love for the Deku Tree and even hung around for a second after it's passing on. You have to think that she was with Deku Tree for a great many years. One day, she is assigned to a young boy by her 'boss' and at his last request, goes to help save the world. She and Link basically grew closer and wiser in their journey. I think that Navi flying off at the end was signifigant that Link had grown up, not needing a guide anymore, for he had saved the land and grew stronger, learning the skills he needed to survive. So she leaves with something of a final, glorius farewell and goes back to the meadow of the Deku Tree, where she sees that all wishes have been fufilled and she has no more purpose in the world. This is when I believe that she passes away in order to rejoin the "spirit" of the old Deku Tree (Think Obi-Wan and Yoda in Star Wars). This also helps to explain why Link was never able to find her in the journeys that took him as far as Termina, where he helps others to grow up.
Now, I haven't read the Zelda wiki article, but there is still no absolute proof that he was searching for Navi.
I base this idea on the Beginning and the end of Majora's mask.
In the beginning, it only says that he was looking for a friend ( I'm not exactly quoting here but) a certain friend that, after he had taken his place among legends, left him.
Now this automatically points to Navi. But, at the end of MM, Tatl speaks. She says something along the lines of "We've both found what we were looking for. I guess it's time for you to leave now, right?"
This is incredibly strange, seeing as Link never found Navi, unless Tatl is the Termina version of Navi, but that's not my theory. My theory is that, most simply, Link was looking for a friend. Now, I know what you're thinking. "Link had plenty of friends" right? Well, let's dive into a bit off psychology... Link, being used to being a hero, most likely felt unfulfilled after he was returned to Hyrule in the Child Timeline. He probably wanted to find Navi, but hat he really wanted was to be a hero again.
Thus, he found Tatl, saved Termina from Termination, and became a hero once more. He found what he was looking for.
Also, he went on this search to further protect the Sacred Realm. If he had stayed there, there would have been a possibility of Ganondorf, or someone else, taking the Ocarina of Time and entering the Sacred Realm. If he left, then no one would get the Ocarina and the Triforce, all together, would be safe.
Afterthought: Even though the Triforce would have been safe anyway since he the Triforce of Courage with him, effectively breaking it, one to Zelda, one to Ganondorf.
I always felt like she died. I don't really know why. But from the first time I beat OoT, back in the day, it was a really depressing scene and I kinda felt like a "passing over" or "on to the next life" kind of exit for Navi. Sort of like the way characters from the Lord of the Rings trilogy take a boat to pass on. It's more or less like leaving for heaven.
What I never got was the way Majora's Mask opened the curiosity back up and gave us hope that she was still alive by opening the game with Link searching for her. Talk about giving us false hope. I was in such a bad mood after beating it because I still had no closure. Even after all of the hinting. In fact I was completely blinded during the first quarter of the game (to how great MM was) because in the back of my head I was like, "Where's Navi! Where the H am I? Where's my horse?! When can I go home!?!
She could have said goodbye or told him to go on with his life, though. It probably would have prevented Majora's Mask from happening.
I think that Link was fated to get to Termina by the Goddesses so he could redeem their world. Therefore, even if Navi hadn't left, they (the goddesses) would have figured out a way to get Link to Termina another way.
Regardless, Navi's exit probably WAS the way the goddesses planned it, or had the deku tree tell navi, or some scenario in which she is aware she must leaving without saying goodbye, so Link WOULD go travel into the woods to find her and eventually find Termina. This is why she left without any parting words; it set up Link's next journey beginning as one of confusion and desperation to find his friend, who left without a word. It lets the mood and scene be set for MM in the right way. If Navi had said anything to Link before leaving, for closure, than Link may have not gone after her after all, having said goodbye. It was the gap leaving the ending open for the sequel, Majora's Mask.