(Additional context: I was asked for my thoughts on many things in this post, among which included what I think happened to Navi at the end of Ocarina of Time. My answer? That she was sent into the future. I must stress that this is not a theory, but a headcanon, as it is based on almost nothing in canon and in some places even contradicts it. But I digress.)
All right. So.
I don’t remember exactly when I first conceptualized this; it’s one of those things that’s been floating around in my head for quite some time, but I only started taking it seriously a few months ago, to the point that I decided it would be a plot point in a fully-fleshed out and realized novelization of Twilight Princess, if I were ever to write such a thing (I almost definitely won’t). It’s ridiculous and ham-fisted and fanservice-y, but the emotional payoff for me is worth it, so I’m willing to let all of that slide in the grand scheme of shoving it haphazardly into my ever-growing non-existent binder that would presumably be labeled “Basil’s Expanded Zelda Universe”. Now, I may not remember the when, but I definitely remember the why - so now that I’ve got all that prattling out of the way…
…let’s actually talk about Navi.
Her departure is as abrupt as it is heart-wrenching, and it’s to be assumed that Link feels the exact same way that the player does. He doesn’t know why she left or where she disappeared to, as his entire journey in Majora’s Mask is built on the premise of him leaving Hyrule in order to find her. And based on how much regret he felt upon his death - regret enough to live on in the mortal realm as the Hero’s Shade - we can assume that he never found her, for all of his searching. (All of this is a given, and isn’t exactly particular to this headcanon, but I felt it was worth saying nonetheless.)
But let’s go back to the moment she actually leaves Link. After Zelda sends him back into the past so he can live out the youth that was robbed from him, he places the Master Sword back into its pedestal, and in the moments that follow, she flies up and away…towards a rear-facing window in the back of the temple.
It’s completely inconsequential. It doesn’t mean anything. It is simply a sign that their time together has come to and close; that their journey to save Hyrule has ended, and Link no longer needs her to guide him. But if you spend as much time as I have putting the same games under the same microscope over and over ad nauseam, you start drawing connections where none should rightfully be made, and in this case, the whole why of the matter…
…is this freaking window.
It’s stupid, right? But there it is again. And it’s not just any window - it’s a portal to the rest of the Temple of Time, a temple that is filled from top to bottom with the symbol of the Sage of Light. But what’s significant about its appearance in Twilight Princess is that this isn’t how the temple actually appears in this time - in fact, it’s completely fallen to ruin - and we as the player have to go back in time in order to even access the inner depths of the temple at all. It’s never specified exactly how far back in time that is, so we’re free to use our imaginations here - like, say…around the time a specific fairy companion left her dear friend without a word or warning.
I’ll just cut to the case.
After the events of Ocarina of Time, Navi ventured into the depths on the Temple of Time, where she awaited and eventually met up with the Hero of Twilight.
Y’see, Rauru was aware that something awry would happen - was happening - in the depths of the temple he himself had built, a small piece of a much larger puzzle that would take at least another century to come into view. As a Sage, he Knows Things - and in Knowing Things he was able to know that Navi had at least one more role to play in saving the Hyrule of tomorrow. Navi never had any intention of leaving Link at the end of their journey; she didn’t want to say goodbye, and in a way I suppose that’s why she never did. When Link - her Link - drew the Master Sword from its pedestal and slept for seven years, Rauru was able to talk to her throughout all that time and inform her of what was going to happen and what she needed to do. Because, as it turns out, if not for Navi’s help, Link and Midna would have never been able to make it out of that place alive…and Hyrule would have, once again, been doomed. (I’m fuzzy on exactly what role she plays in helping them, but I’ll figure something out soon enough; I always do.)
So, she leaves him. The Hero of Time. In the sword chamber. And she doesn’t say goodbye, because she doesn’t want to, and it’s painful, but it won’t be forever, right? Once she finishes what she has to do, she can go back and be with him again, explain why she left, why she had to leave. Except…
…something goes wrong.
And she can’t go back.
After Link and Midna retrieve the third fragment of the Mirror of Twilight, they’re forcibly removed from the temple - they don’t belong in this time, after all - and once the door to the past closes behind them, it closes for good. And Navi…gets swept up with them.
She’s a nervous wreck, of course. So much about Hyrule has changed in the years she’s been gone. (”I’ve seen the future before, but not like this!”) But, nervous and fretful as she is, she’s also quite resolute, and no matter how much time has passed, there’s still something she needs to do. Or, rather, someone she needs to find. She bids the Link of this time farewell, and goes on her way.
Sometime shortly after the events of Twilight Princess, we know that Link returns the Master Sword to its pedestal in the ruins of the Temple of Time; we see as much in the final credits. I’ve always liked to think that, when he did so, he got to see the Hero’s Shade one…final time. For all the regrets the spirit had eased - Hyrule was safe, now - there was still…one thing he had left to reconcile. It was here that he last saw her, after all. Of course he would find his way back to this place. And maybe - maybe she would, too. Maybe…
