The Legend of Zelda: Ocarina of Time has been around for a long time now, but it remains one of the games with a lot of unanswered questions. It seems we aren't the only ones to notice that, as even Miyamoto feels that there were things left unsaid. It is likely to be a long time, if ever, before we find out the answers. The mysteries that remain would give us a few solid answers to the franchise.
The lore of the Legend of Zelda series is confounding at the best of times, even with the answers we do have. Due to the nature of the games, it will likely always be that way, as things rarely ever get clearer. I think some fans enjoy that speculation and enjoy attempting to unravel things on their own, or at least I do, but sometimes the mysteries are too big, and it makes the quest to understand the lore harder than it should be.
Miyamoto Said A Lot Of Mysteries Were In Ocarina Of Time
Even He Was Left Unsatisfied By The Unresolved Threads
An interview translated in shmuplations from a Japanese strategy guide gives us a little insight into what Miyamoto was thinking as Ocarina Of Time was in the process of being made and shortly after release. Specifically, in one question, Miyamoto agrees that he was unsatisfied with several of the things that were hinted at but never stated in the game. This includes Ganon's background and whether or not Link is the same Link or is otherwise related to the original Link in the first game.

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He said that these mysteries perplexed him as the game was being made, and many of these questions continue to go unanswered. While Ganon seems to be a resurrecting villain who just continues to come back, other questions remain a little unclear. The timeline of Zelda is a whole question on its own, even after Nintendo made official announcements regarding it. It's a hard franchise to pin anything down on, which seems to be intentional as Miyamoto said that he cares more about an interesting game than intra-series continuity.
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While some of the mysteries have been solved, others remain just as murky, or murkier, than they were before. Ganon in Legend of Zelda is one of the clearer entities at this point. For a long time, there was debate over whether or not Ganon and Ganondorf were the same entity or not, and it appears they are. The names are used interchangeably throughout the series, and the Demise Curse seems to ensure that Ganon will continue to reincarnate in some form or fashion for a very long time.
However, just because he feels clearer doesn't mean things are completely ironed out. It remains a question as to how Ganon was born of the Gerudo as well as how he truly became what he was - and later how he became Calamity Ganon. There are a lot of different options that will likely be debated for a long time to come. But Link is another persisting problem.

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Whether or not Link is related to the original Link in the first game is still a mystery, and it seems unlikely that this will change. We know that Link from Ocarina Of Time is also present in Majora's Mask. We also know that his ghost is likely who appears in Twilight Princess, but other than that his relation to the remaining Links in the Timeline(s) is unclear. Sometimes Link and Zelda are descendants of their previous appearances, but sometimes they are reincarnations but unrelated. Other times it seems like they may be mostly unrelated, save for some shared characteristics.
It's unfortunate to me that many of these remain in the dark. It would be nice to see a bit more about how Link and Zelda are connected to each other and to the other versions of themselves. That is one mystery that hasn't changed, and, in fact, got more confusing with Breath of the Wild and Tears of the Kingdom, which may not be on the main timeline at all. I would like a little more clarity, but given the current state of the franchise that seems unlikely.
Will Future Zelda Games Address These Ocarina Of Time Mysteries?
Is There Hope For Those Waiting For Answers?
In of the Link in Ocarina Of Time, the only way that I foresee the mystery changing is if we get another remake of that game where they can address it. Ganon might be a better possibility, as we did get some answers in Tears of the Kingdom and even the interview states that he just keeps coming back regardless. It also depends on where the franchise goes next, if we get another big title like Breath of the Wild. We are fairly certain that it won't be a sequel, and that it will be a standalone game, so it could address any moment in Zelda history, and we could get some answers that way.
I would like to see a Ganon-centric game where we see exactly where he comes from and more about his history among the Gerudo, being the only male that exists. If this happened, we might also get more clarity on just how the Demise Curse comes to him and how exactly he and Ganondorf are interconnected. There are a lot of possibilities with a game like that, where he isn't necessarily the antagonist, and I believe there would be a big enough fanbase to justify a standalone game like that.
Otherwise, I think most of the mysteries from Ocarina Of Time will stay mysteries unless we get a second remake or a direct statement from Nintendo. The mysteries Miyamoto addressed specifically likely wouldn't come up in another game, as the timeline splits from there and anything following one of those timelines would only address that version of events. However, with the amount of remakes happening these days and with the Switch 2 coming, it doesn't feel impossible to say that these mysteries in The Legend of Zelda could be solved sooner than we think.
Source: shmuplations

The Legend of Zelda: Ocarina of Time
- Released
- November 21, 1998
- ESRB
- E10+ for Everyone 10+: Animated Blood, Fantasy Violence, Suggestive Themes
- Developer(s)
- Nintendo
- Publisher(s)
- Nintendo
- Engine
- Zelda 64 Engine
- Franchise
- The Legend of Zelda
- Platform(s)
- Nintendo 64, GameCube
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