Zelda Theory - Saria is Missing
I'm pretty sure I'm not the only one who believes this, but I'm still going to put it out there. It's my headcanon really, I believe that in Majora's Mask, Link is actually looking for Saria, not Navi.
Of course, Nintendo's official stance is that he was looking for Navi, but keep in mind that Nintendo used to say there was only one Link in all the games. What I'm saying is that they can change their mind whenever they want.
Really, there's only two data points to back up my theory.
First, let's consider how vague the instruction booklet is about why Link is looking for someone:
"Done with the battles he once waged across time, he embarked on a journey. A secret and personal journey... A journey in search of a beloved and invaluable friend... A friend with whom he parted ways when he finally fulfilled his heroic destiny and took his place among legends..."
A beloved, invaluable friend that he hasn't seen since the end of Ocarina of Time. That could refer to Saria or Navi.
But, I find it hard to believe Navi could be called Beloved. How long did he know Navi? A month? Three months? And he very clearly sees Navi leave at the end of Ocarina. Are we supposed to believe that she left without saying a word? I mean, if they were close enough that Link thinks of her as Beloved, she would have told him something.
Meanwhile, imagine that Link goes back to the Sacred Forest Meadow and Saria is gone without a trace. She's not in her house, and not even in the Forest Temple.
Remember, Saria says that it is destiny that they cannon live in the same world. Sages become Spirits when they're awakened. (The Japanese call this Kamikakushi - spiriting away.)
Now, the second data point is at the end of Majora's Mask. At the end of the game, the Skull Kid says Link -
What a weird way to cap off the game, don't you think? I mean, according to NIntendo, Link was looking for Navi this entire time and we end with "You smell like a sidequest."
We're supposed to assume that this is the same Skull Kid that appears in the Lost Woods that you can "teach" Saria's Song to.
But, here's the thing, that doesn't happen unless you do that Sidequest. You could completely miss it if you don't go exploring.
So, my stance is that it was Saria herself that taught the Skull Kid the song, since she spent so much time in the Lost Woods. It would make more sense, narrative wise, that Link was looking for Saria, and the game ends with "You smell like Saria. I was friends with Saria. We should be friends!" (Obviously, I'm reading between the lines)
Majora's Mask is a game about the little things. It's about how people affect each other's lives, and no matter how isolated we may seem, we're all connected. Just like Link left an indelible mark on Termina, Saria affected those around her, too. Even in their absence, the people we care about still affect us today.