The Legend of Zelda: Ocarina of Time/WMG

Sheik came from a Sheikah Mask
Warning: some spoilers may be unmarked! (and for those of you who wanna see the spoilers, you can just highlight the text with your mouse and cursor)
 * In the game Majoras Mask, which is the direct sequel to Ocarina of Time, Link uses various magical masks to transform himself into different beings. Each mask was created when a member of the race it represented . The Goron Mask came from a great Goron named Darmani; the Zora Mask came from Mikau, the guitarist of a Zoran rock band called Indigo-Go; and the Deku Scrub Mask was implied to come from the unnamed son of a butler at the Deku Scrub Palace. Whatever form Link is in, he still maintains certain key traits of his original form (mainly the green tunic and his trademark hat).
 * Now, let’s think about the Sheikah. Princess Zelda’s nanny, Impa, is a Sheikah, and apparently the last of her tribe. Impa has red eyes, and, although she doesn’t look very old, and seems to still be in very good physical shape, white hair. Since the Sheikah tribe never actually appears in the game, it is possible that this coloration is - was - typical of the Sheikah people.
 * As this Wild Mass Guesser mentioned before, in Majoras Mask, Link still looks somewhat like himself in any form. So Sheik,, would maintain his blond hair.
 * Also, about Sheik: the Sheikah, judging from Impa’s getup, wear very skintight clothing, probably to help them sneak around better (kind of like ninjas). Being a tribe based on Shadows, going unnoticed would be very important for spying.
 * So, if was simply dressed as a Sheikah man, wouldn’t  physical characteristics as a  show through a skintight suit? This Troper thinks so.
 * Conclusion: Sheik was once an actual Sheikah warrior. He was killed in battle, and, as a desperate attempt to save him, Impa sealed his soul into a mask.
 * Why? Maybe he was her son.

Re Dead behavior
When the player kills a Re Dead where there are other Re Deads around, the others will gather towards the fallen one and crouch down. This could mean they are doing one of two things:
 * Mourning.
 * Devouring.

The Sages are all dead
This is never stated outright, but heavily implied. Think about it. All of them disappear at some point before you face the boss. All of them Ascend to A Higher Plane of Existence. This is most telling when Saria says she'll always be with you, and during the end credits when the sages are watching over the party at Lon Lon. They don't join; they just hang out for a while, exchange a few sentimental glances, and then sparkle off into the distance. Fridge Horror Tear Jerker for this troper.
 * ...except they don't sparkle off into the distance. The cutscene fades to black before the Sages actually go anywhere, so they could just as easily have come back.
 * But when you think about it... Darunia entered Volvagia's boss room before you had a chance to. And then when you finally get there, Darunia is nowhere to be found...
 * You can talk to Saria all throughout the Forest Temple. Kotake and Koume teleported Nabooru away, they didn't kill her, and their Twinrova form is used in the Oracle games as well, so Nabooru wasn't a component of it. Plus, the only reason the sages weren't awoken immediatly was because Ganondorf cursed the temples and they couldn't awaken as sages until the boss monsters were killed and they could hear the call. Saria was sad because the sages had to live in the Sacred Realm, at least until they had to seal Ganondorf into it, at which point it may have been to dangerous for them to stay in it.
 * (Spoiler Alert) However, in Twilight Princess, the sages do not have physical bodies, they are just spirits, and one of the sages actually dies. Ganondorf lashes out at the sage of water and he just dissapears, never to be seen again.
 * We're not talking about the TP sages. And whether or not they're one in the same as Oo T's sages is a whole other debate.

The game is the origin of a Merlin-or-Gandalf-like wizard
Not much to explain here. A Hylian raised in a Hidden Elf Village, saving the whole kingdom and learning a bunch of magic spells and skills along the way. In the kingdom of decades later, if the young hero is now an old one, he could certainly remain as a white-bearded bastion of hope and the ways of magic. Even if he's the king too!

The reason the well got sealed up during the seven year sleep
Some kid went in there sometime after kid Link went to sleep and saw the horrors within. After escaping and telling people about it, the well got sealed up.
 * Could be the kid from the graveyard? Had an obsession with the morbid, and when we next see him he's (possibly) the insane poe collector... Entering the well finally broke him?
 * I was under the impression that the Poe collector was the same guy as that castle guard from 7 years prior (he was in the same room, and if you pestered him at the right time he'd mention he was a paranormal enthusiast). On the other hand, that still doesn't quite explain that kid's whereabouts... maybe the well was sealed because he went in, but he DIDN'T come out. Then someone went in looking for him, and...
 * There's always Dead Hand

Malon was going to be the Sage of Spirit
This just hit me before posting. Consider: Nabooru isn't met until it's time to enter the Temple; the Gerudo Mask reminds Talon of Malon's mother (who is theorized to have been Gerudo because of this line); all the other Sages are met before you open the Door of Time, except Rauru, who's first met the instant Child Link pulls the Master Sword from the pedestal. (unless he's Kaepora Gaebora). It's plausible that Malon was going to be the Sage of Spirit, awakening as a Gerudo over the timeskip. Bonus points for being part of Link's harem along with Zelda, Saria, Ruto, and Nabooru.
 * However, save for the red hair, she doesn't look like a Gerudo at all. It's possible that it was planned that she was going to be but was changed into a Marin expy later on. Or, perhaps Gerudo children look like Hylians until they're about in their early twenties or so? But that's it's own WMG...

In Master Quest, Ganondorf fed Jabu-Jabu with cows to spread mad cow disease
And then the sickness got so bad it spawned electric jellyfish plus the boss. Even worse yet, said cows merged with his internal skin to become animal switches to make Link feel bad and lose all his confidence to continue his quest just to open a measly door. Yes, Ganondorf thought about everything.

== Alternatively, the cows were the same cows "Them" stole from Romani Ranch and accidentally put them in Jabu-Jabu with Romani as well. Romani was so traumatized by this event that she later escaped from the fish's belly and changed her name to Malon to live a new life == Darn aliens are now messing the storyline by going back in time.

The Poe Collector is the guard from the same lookout station in the child Link period
Not only they stand at the exact location, but also both enjoy chaos. The guard says he wishes things were more chaotic while the Poe Collector is very happy that Hyrule is now in chaos. Moreover, the robes the Poe Collector wears bear the Triforce symbol, indicating that he was once involved with the Royal Family prior to Ganon's overtake of Hyrule.
 * Basically confirmed when you return to the past and talk to the guy, and he reveals he's a bit of a ghost enthusiast. (In the remake, at least- I don't 100% remember if this was in the original, but given that not many lines were changed/added, it probably was.)
 * It was in the original version, and you don't have to return to the past for him to say that, it just has to be night-time. He'll say that anytime in the game you visit him as long as it's night-time.

Alternatively, The Poe Collector is the kid Link sells the Spooky Mask to.

 * Note that he does not appear at all in the adult Link period, both of them carry a stick, both like scary things, and the kid wanted to be "heart-pounding". Also, the Spooky Mask resembles a Re Dead, which populate Hyrule Castle Town.

Farore's Wind, Din's Fire, and Nayru's Love are the cut powers of the Forest, Fire, and Water Medallions
For those not in the know, a beta screenshot had the Forest Medallion equipped to a C button, implying it could be used as an item, possibly as a neat spell. Obviously, that didn't make it into the final game, but it's entirely plausible that some of those powers were partly implemented before the concept was cut. Since game programmers hate to waste code, they decided to work what they had into separate items, becoming the fairy spells currently in the game.

Why those Medallions specifically? It seems thematically appropriate.


 * It's also theorized that the Spirit Medallion became the Lens of Truth.
 * That fits, because even though you complete the Spirit Temple last, there are several in-game instances in which Spirit is listed before Shadow. And since you need the Lens of Truth in both temples, maybe this was a change that was made late in development...
 * The Light Medallion could be the Mask of Truth.
 * Further evidence that could support this: the entrance room for the Shadow Temple involves a torch puzzle that requires the use of Din's Fire. However, the platform Link must stand on to be properly placed for this spell has an image of the Fire Medallion on it, even though nothing else about the room seems linked to the Fire Temple in any way. Given the developers' tendency to plant visual clues to the solution of a puzzle, it's likely that the medallion image was placed there so the player knew which item/spell to use. Therefore it could be assumed that the image wasn't removed when the medallion-as-spell idea was scrapped, but that the solution spell itself remained in the form of Din's Fire.

The Gerudo captured the carpenters in order to use them for procreation
The Gerudo only have one male child every 100 years. In fitting with their overall Amazon theme, they would naturally kidnap men in order to procreate. Makes you have second thoughts about Link's "rescue" mission...although admittedly, the Gerudo would probably would kill them afterwards, just like the original Amazons.
 * Well, I think one of the Gossip stones says that the Gerudo go into Hyrule to "get boyfriends"... So this is pretty darn plausible of a WMG...

Navi is trapped on an infinite time-loop
From the beginning Navi is conveniently aware of the names of your enemies and their weaknesses, as well as showing you any place of interest inside a dungeon, etc. But how did she came up with this knowledge? Well, she's trapped in a time-loop of course. At the beginning of Majora's Mask we learn that Navi disappeared after Link returned to his childhood. What if she went further back in time? Specifically to the time at which OOT begins. That would explain not only her knowledge but also the reason why Link didn't have a fairy before that moment, because Navi didn't exist until that point.

Darunia (the Fire Sage) is a female Goron
The gorons have no gender differences and all address each other with male pronouns regardless of gender. And that would make only one male sage among the seven: the old man you first encountered at the Light Temple!
 * I'm sorry, WHAT?
 * That could work, except for the part where Darunia expresses himself as a male ("We are brothers") and the part were the Goron named after you asks you to rescue his Dad.

Location, Location, Location
In between Ocarina of Time and The Wind Waker, there was a Great Flood, which turned Hyrule into the Great Sea. Although most of it was underwater, many of the islands and locations seem to be remnants of the drowned kingdom. (And as for how those places became islands instead of staying underwater - the Goddesses raised them up.) "Once upon a time, long ago, the Koroks took on human forms, but when they came to live on the sea, they took these shapes."
 * The Gerudo Fortress = The Forsaken Fortress
 * Castle Town = Windfall Island
 * The architecture on the island seems to resemble a castle. The resemblance to Kakariko Village is due to the residents of Kakariko moving to Windfall and rebuilding their homes. Eventually, the sub-cultures/architecture of the people from Castle Town and Kakariko Village merged, and they created Windfall.
 * Death Mountain = Dragon Roost Island (& Fire Mountain)
 * In Twilight Princess, it’s implied that the Gorons don’t need to breathe, and can stay underwater indefinitely. So most of them may have felt no need to evacuate to higher ground when the Flood came. (The three travelling merchants - all clearly Gorons - located on Greatfish Isle, Bomb Island, and Mother and Child Isles remain on the surface for business purposes.) So the Gorons stayed in Goron City.
 * The Zoras, on the other hand, despite being highly adapted to aquatic environments, weren’t so lucky. Although they seem at home in the water with their fins and gills, their humanoid bodies imply that they aren’t meant to be in the water all the time.
 * In real life, most fish are meant to be in either saltwater or freshwater; only a few, like bull sharks, can swim and breathe in both. Some of the Zoras, by praying to the Goddess Nayru, were able to adapt quickly to the saltwater environment, and settled on Greatfish Isle . To thank Her, they created Nayru’s Pearl, which housed some of power of the Goddess Herself. They also hatched, nurtured and raised Lord Jabun, the offspring of the demi-god Lord Jabu-Jabu, to watch over them as the new living Water Spirit.
 * The other Zoras travelled north to the top of Death Mountain, and turned to the Goddess Din for aid. In answer to their prayers, She gave them avian features (beaks, feathers, wings) to protect them from the scorching heat, and entrusted a dragon egg to them. This egg held the single surviving offspring of the dragon Volvagia, who was slain by the Hero of Time. When the egg hatched, Din deemed the newborn dragon to be Lord Valoo, the living Sky Spirit. The Zoras, no longer being Zoras, began to call themselves Ritos, in memory of Ruto, the Princess (and later Queen) of the Zoras in ancient times.
 * Although the Ritos had wings, their wings were not big or strong enough to enable flight. So Din instructed Valoo to give each adult Rito one of his scales (which grew back easily). These scales triggered a magical “growth spurt” that caused a Rito’s wings to grow big enough to allow flight. Eventually, it became customary for young Ritos to visit Valoo and receive their wings when they came of age. To thank the Goddess for Her kindness, the Ritos created Din’s Pearl, which housed some of the power of the Goddess Herself.
 * Kokiri Village & The Lost Woods = The Forest Haven & The Forbidden Woods
 * When the Great Flood came, the Kokiri were completely unprepared. They were afraid to leave their forest, and couldn’t bear to abandon their guardian, the Great Deku Tree. The Deku Tree, who had just reached his juvenile stage of growth, prayed to the Goddess Farore for aid.
 * The Goddess answered by taking away the burden of the human forms the Kokiri took on. They shed their mimicked humanoid features and became what they had always been underneath: the Koroks.
 * The Kokiri, despite their mammalian appearance, had always been sentient plant-people. Instead of blood, they had chlorophyll keeping them alive. When they became the Koroks, they became lightweight enough to use the leaves that the Great Deku Tree shed as makeshift “wings”.
 * To thank the Goddess for Her kindness, the Koroks created Farore’s Pearl, which housed some of the power of the Goddess Herself.

--The Great Deku to Link, when the Koroks reveal themselves.

The Forest Temple is actually the Temple of Time from Twilight Princess
Think about it - it's in the depths of the Lost Woods, it's an overgrown, ruined building, and we already know that the Master Sword has resided in the Lost Woods at least at one other time (Link to The Past). Given that Twilight Princess appears to have you taken back to the past to obtain the sword, this would suggest that it is the original resting place of the sword, and that it was moved to the Temple of Time in Ocarina of Time more recently. Note the twisting corridors in the Forest Temple, similar to those seen when travelling to Termina - this suggests that the Forest Temple actually links to another realm, likely the Sacred Realm. Indeed, it is plausible that the Sacred Realm is connected to all of the Temples, as those are the places that the evil emanated from when Ganondorf got the Triforce of Power. Note that what would become the Forest Temple in Twilight Princess is actually the Great Deku Tree, so they are not the same temple.

Oot Link is stuck in an endless time-loop in the Adult Timeline.
At the end of Oot, Zelda sends Link back in time to live the skipped 7 years of his childhood, leading to Majora's Mask. However, she doesn't know that she sent him back after Majora's Mask. So after every time Link defeats Ganondorf, Link is sent back in time to continueously live through MM. This leads to him disappearing and the events of Wind Waker.

The Link and Zelda from Ocarina of Time are twins.
We know from the Great Deku Sprout that Link's mother was a Hylian who fled to the Kokiri forest under unpleasant circumstances. Based on what little we see of her, she seems to have been a noble of some sort (why else would someone have been gunning specifically for her and her family?) The King of Hyrule has a couple of offscreen "appearances", but the Queen isn't even mentioned. Link and Zelda are around the same age, and both have blond hair and blue eyes in a world that, if you look closely, seems to be populated by people with every possible eye/hair color combination but blond hair and blue eyes. They also seem to have a telepathic connection of some sort (Zelda's dreams, and the vision that teaches Link the Song of Time) before they wound up with two pieces of the Triforce embedded in their hands. We also know that there was a long and bloody war between the Gerudo and the Hylians prior to the game's story. And wartime is when a nation's rulers are at the greatest risk; everyone knows that when you cut off the head the body dies. Conclusion: The Royal Family of Hyrule came under attack by assassins, and the Queen was forced to flee along with her son. For whatever reason, she didn't bring her daughter or husband. (Perhaps they were separated in the confusion? Or maybe they needed to have both a ruler and a clear successor to the throne to prevent total anarchy, and the Queen went into hiding with one of the two heirs in case the King and Zelda didn't make it...) Anyway, she wound up in the Kokiri forest, died of illness, injuries, or just plain exhaustion, and Link was raised by the Kokiri to become the green-clad hero we all know and love.
 * The King stays behind to lead during war. Zelda goes into hiding with Impa. The Queen takes Link (who as the male would have been primary heir even if Zelda was actually older). The split betters the chance one heir would survive should something go wrong during the escape.
 * Word of God confirms that pointy ears are a sign of the royal family of Hyrule. Can you think of a certain Hero of Time with pointy ears?
 * Gonna have to call foul on that, or at least ask for a source. A quick check in Ocarina of Time shows that everybody and their brother has pointed ears. All the Kokiri, all the Hylians, Impa, Malon, Talon, Ingo, Link, Zelda. . . Even Ganondorf gets in on the elfy-ears action, post-seven-year Time Skip. Link and Zelda have have a whole lotta siblings, aunts, uncles, and cousins if that were the case, is all I'm saying.
 * You left out the part about Link's name being familiar to Zelda even though this is the first pair and it was the first time they met.
 * Cue thirteen years later.