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    Concerning Link 
TP!Link is Rusl's younger brother.
And, tying in with the "Colin is ALttP!Link" WMG that used to be on the main Zelda WMG page (could someone who saw it reproduce it here or on the series WMG page?), he's the uncle who bites it at the start of ALttP. Further evidence that Link's only mute when he's the player character.
  • Well, the trading cards do say that Rusl thinks of Link as an adopted younger brother...
  • They would have to be half-brothers to account for Link being at least part Hylian while Rusl is clearly not.
    • Jossed by Hyrule Historia. TP and ALTTP are on completely separate timelines and do not connect.

This Link is a descendant of Malon and OoT/MM!Link
This Link has Epona and is a rancher. The Hero's Shade, who happens to be the Hero of Time, also refers to him as "my child" a few times, which may be endearment or not. He also said that only those who carry the blood of the hero can use certain moves and he also once said "our bloodline". Malon was also the only female Link knew who he could have copulated with. MM!Link eventually married Malon, had children with her, went to search for Navi and got lost in the forest. TP takes place 100 years before TP so he could be their grandchildren. Malon hasn't been reincarnated yet either.
  • As a Link x Malon shipper I am for this theory. The only problem is that Link went to Termina less than a year after The Legend of Zelda: Ocarina of Time, and he was 10 at the time. We'll just assume he settled down with Malon after getting back.
    • Well actually, one theory on this page makes reference to Fado's lines from OoT: that everyone who gets lost in the Lost Woods becomes either a Skull Kid (if a child) or a Stalfos (if an adult). Link searched Termina as a child and couldn't find Navi, so it's easily possible he went back, had children with Malon, then went into the Lost Woods where Navi might be. Having no fairy rendered him susceptible to the Lost Woods' influence and got, well, lost. Then he became a Stalfos. The Hero's Shade is a skeleton, as are Stalfi, and they wear armour that are similar in appearance. Link was also blessed by the Triforce of Courage, so while he became a Stalfos he kept his humanity and lingered in the world of the living. Make sense? I thought so too.
      • Also, given how The Hero's Shade is clearly more like a Stalfos than a Skull Kid, it means that OoT Link had time to settle down with Malon.
      • Comments made by Eiji Aonuma place the Hero of Twilight as the son of the Hero of Time, meaning that the Hero of Time didn't get back to Hyrule from Termina until a long time after everything...

    Concerning Midna 
Every Hylian has a Twilight counterpart; Midna is Zelda's.
First, she's a princess, second, her Leitmotif is Zelda's Lullaby played reversed. Also, her personality bears some great resemblance to a certain girl who turned out be a Zelda raised by Pirates. Whose counterpart is Zant then? Believe it or not, I think, based on some theories that Zant was actually Midna's lover before Ganon took control of him, that he's actually Link's counterpart. Would explain why she supposedly fell in love with Link over the course of the game. She probably destroyed the mirror out of fear that, now that her beloved Zant was gone for good, she would not be able to resist to go back and see Link. Another reason for that speculation: Midna's name has the same number of letters as "Zelda". And Zant's name has the same number of letters as "Link". Of course, the Zant part is not very well-grounded, but I'm pretty sure about the Midna part though.
  • Also, check the form of the words. Zelda and Midna are both two syllables, one ending with a "d" sound and one ending with "a". Link and Zant are both sharply terminating syllables. I doubt this is the case, since the Twili are descended from people kicked out of Hyrule via the Twilight Mirror, but it could be like Peirs Anthony's Split Infinity where the worlds aren't perfect mirror worlds, but anyone who has a proper background in one is more likely to have a counterpart in the other. I'm of the faction that thinks Midna looks like she's distantly (or not so distantly) descended from the Gerudo, the likelihood being increased in that the Gerudo were both one of the few races Hylian law included as well as the most likely to be criminals (or at least considered criminal), so it would be poetic considering Ganondorf's possible motivations from Ocarina of Time.
  • It's also worth noting that Zant seems to be more courageous than the other Twili, with his desire to reclaim what had been taken from his people. Unfortunately, he was lacking in wisdom or the support of the wise, and bolstering his innate courage and Twili power with more power, and corrupted power at that, was not the correct solution.

Midna is speaking in Hylian
Her "gibberish" is really just what Hylian sounds like in Twilight Princess.

Midna is the reincarnation of Hylia in this era
Skyward Sword reveals that each set of Zelda and Link are the reincarnations of the Goddess Hylia and her lover/general. But in TP, Zelda seems almost secondary and the emotional connection is between Link and Midna. So maybe this time, Zelda was just a random soul, and Hylia was reborn as the Twilight Princess, but still found her beloved.
  • Debunked due to the fact that Hylia is not the one who reincarnates; only Link is. Hylia's power is only passed down through the bloodline of Hyrule's royal family.

Midna is the TP incarnation of Impa
It's heavily implied that the Dark Interlopers were the Sheikah, with the Sheikah symbol even appearing on Zant's (actually Midna's) throne, minus the teardrop said to represent sorrow and regret. Both Zant and the original king of the Twilight Realm were power hungry, and after the old king's attempt to use the Fused Shadows to overthrow Hyrule was quashed, the remaining Sheikah, even the innocent ones, were banished to the Twilight Realm, joining those already there (Impaz is spared because she's secretly only half-Sheikah and so lacks the tanned skin and red eyes all other Sheikah have, causing the soldiers who invaded the original Kakariko Village to think she was Hylian, thus allowing her to evade capture). This included Impa, meaning Zelda lost her friend, mentor, and mother figure for no good reason, leaving the princess bitter and emotionless. Impa, now banished, retook her place as the rightful ruler of her tribe. In her shame over what her people had become, she renounced her name and took a new one, and later the Twilight realm changed her form into that of a Twili just as it had done to the rest of her tribe. Her taking power angered Zant, which lead to the events of the game. Zelda's sudden expression of sympathy and kinship towards Midna is because she realizes who Midna used to be and is her last ditch effort in attempt to dissuade Midna from destroying the only link between their worlds. However, Midna is still too ashamed of her tribe's blood-soaked past, and she shatters the mirror out of belief that it is what she and her people deserve.

    Concerning the Hero's Shade 
The Hero of Time became the Hero's Shade after his own set of adventures and kept some of his items before his passing
It's not too implausible to think that Link from Ocarina of Time decided to have his own adventures as an adult in the child timeline, despite not being remembered as a hero. More importantly, Colin's father own the iron boots, which OoT Link used when he was an adult. As far as the third timeline from A Link to the Past and Oracle games show, he may have been in another country/continent at the time. And since you can't really have a descendant without passing on your genes, perhaps at one point, Link's concept of romance developed and married one of the only three girls he knew (Malon, who is the most popular theory and candidate). Before his passing, he may have gave away his boots to one of villagers who would be Colin's grandfather.

Ocarina of Time Link returned to the Kokiri Forest/Faron Woods/Lost Woods to die.
Later on in his life, OoT Link probably wanted to die and/or be buried in the forest, which was his home and where he was raised. He was probably very sentimental about it, as typical of a hometown. That's why you first meet with the Hero's Shade in the Faron Woods.
  • This makes sense, since the Hero's Shade resembles a Stalfos, which non-Kokiri apparently turn into after long exposure to the Lost Woods. Since OoT Link is Hylian and not Kokiri...
  • There is also the remote chance that he had fallen in love with Saria, and overlooked the obvious Squick.

The meetings with the Golden Wolf/Hero's Spirit aren't actually happening.
Building on the above theories, the Golden Wolf doesn't actually exist in the physical world. In actuality, the meetings with the wolf are just a visual metaphor for memory. Not once in all the meetings does Midna ever appear, and no matter how long Link takes to learn the new skill, no time ever passes in the real world. The only clear explanation is that he's subconsciously accessing memories from his past life.
  • It follows that the memories are sparked by hearing a familiar bit of a song as the wind whistles through the hollow stones, which he placed there in his previous life's later years for expressly such a purpose.
  • Midna does appear in the Golden Wolf meetings, but she doesn't say anything, so... maybe you have a point.
    • When does Midna appear in these encounters? You can't call upon her when you're learning a Hidden Skill...at least, not that I remember.
      • You can't call upon her and she doesn't talk, but you can see her sitting on Link's back when he howls the duet with the golden wolf. As for when you meet the golden wolf as a human to learn the skill, I would assume she's still there hiding inside Link's shadow as usual.
      • Well, that's because at that point in time, Link's used to having Midna on his back, so therefore that's how he may see it during these duets with what truly may be an imaginary character. Really think about it; if you're having dreams that include yourself in it and you know for a fact what you look like, how likely is it that you are going to be altered?

The Hero's Shade, aka the Hero of Time, aka OoT/MM Link, is directly responsible for TP Ganondorf obtaining the Triforce of Power and surviving his execution
The one thing that has consistently bothered me about Twilight Princess is that there's no reason for Ganondorf, Link, or Zelda to have their respective Triforce pieces as, in the Child Timeline, the Master Sword was never drawn and the Sacred Realm was never breached. Nobody ever laid a hand on the Triforce, so it could never have split and found its way into the main trio's hands. Unless somebody did.

After Link returns from his mysterious sojourn in Termina, he tries to re-integrate himself into normal Hyrulean society in a time of peace and prosperity. Perhaps he succeeds at first, being a young, good-looking lad who benefits from a close friendship with the universally-adored Princess Zelda. However, as time goes by, he grows less and less satisfied with his lot in life. The problems and complexities of adult life begin to weigh upon him, and he yearns for the simpler life he knew as a child when everything was black and white: he was the good guy, and the monsters were the bad guys who needed to be killed. He misses the courage he had as a hero. So he sets about re-embarking on the quest that set him on that path in the first place. He re-acquires the Spiritual Stones, opens the Door of Time, and draws the Master Sword. He enters the Sacred Realm and ascends the Temple of Light to the summit, where the Triforce is held, and attempts to take possession of it and make his wish: to once again be the great hero he once was. However, as always happens when someone with an unbalanced heart touches the Triforce, it splits into its three components: Link retains only the Triforce of Courage; the Triforces of Wisdom and Power go to the two people in Hyrule who most embody those virtues: Zelda and Ganondorf.

Ganondorf, having been languishing in the Arbiter's Ground prison these long years, has finally been marked for execution. The sages drag him to the top of the prison and prepare to do the deed, but just before the stroke falls the Triforce of Power finds its way into Ganondorf's possession. The execution fails, Ganon is banished to the Twilight Realm, and the events of Twilight Princess ensue. Link, meanwhile, ashamed at what his greed has done, vows to walk the earth forever, until he can help a new, purer hero to rectify his mistake.

  • Debunked. Ganondorf did receive the Triforce of Power thanks to Link, but Link didn't knowingly do anything that led to it. When Zelda returned him to his childhood, the Triforce of Courage remained with him, thereby causing the other two pieces to go to their respective wielders.

The Hero's Shade is Dark Link
He's got red eyes like Dark Link, knows a lot of fancy moves which OoT Link has never demonstrated and he is Link's (the hero) Shadow (shade). Why is he helping TP Link? Presumably like Phantom Ganon, Dark Link was banished to the gap between dimensions and is reaching out to help Link kill Ganondorf so the curse will be broken and Dark Link can be released and do his own thing.
  • Jossed. The Hero's Shade is OoT Link.

The Hero's Shade isn't actually a Stalfos, he just takes the form of one to train Link.
Considering that he's a spirit and not a corporeal entity, and also appears as a Golden Wolf, it's entirely possible that he can take whatever form he pleases. He simply chooses the form of a Stalfos so that his descendant won't feel bad about attacking him.

The Hero's Shade was killed by a Darknut

While everyone immediately picks up on the Stalfos connection in the appearance of the Hero's Shade, there's something else, too. The Darknuts of Hyrule Castle also have some resemblance to the armour of the Hero's Shade, particularly the helmet and the shield. There's plenty of theories as to where they came from, with one popular one being that they were creations of the Hylian Royal Family, or a military faction tasked with protecting them Sheikah style. Perhaps they were modelled on a fully grown Hero of Time? Given how he remained an exceptionally skilled swordsman and had a number of adventures, and was Zelda's friend, he'd probably have caught the eye. In that scenario, perhaps they went rogue, with one (or several) of them killing him as an adult - perhaps a relatively young one, old enough to have a child but not old enough to train them (explaining his regret at not passing on his skills). Alternatively, he's armoured like them because they played a key role in his death.

Either way: he was killed by one or more Darknuts. Considering how formidable they are, and the fact that the Hero's Shade is notably missing an eye (suggesting a lack of depth perception), it's certainly plausible.

Additionally, it's also worth noting that several of the Hidden Skills the Hero's Shade teaches Link are directly relevant to fighting the Darknuts: as early as the third one, he makes a very specific point about fighting fully armoured enemies, and teaches Link the Back-Slice, despite the fact that the lesson comes after the Goron Mines, and before the Lakebed Temple - the second and third dungeons, respectively. While a fairly useful move in general, especially against King Bulbin in the Gerudo Desert, it doesn't really come into its own until you're faced with an armoured, sword-wielding enemy - a Darknut. That doesn't happen until the Temple of Time, which isn't the first, second, or even third dungeon after the Goron Mines, but the FOURTH.

And that's not the end of it. Immediately after the Back-Slice, the next move he teaches you is the Helm-Splitter, a move also most relevant against armoured swordsmen, like, again, Darknuts. This one is just before the Arbiter's Grounds, the fourth Dungeon, as is the next one, the Mortal Draw - also, to a lesser extent, mainly relevant against powerful enemies like the Darknuts, and perfect for dealing with their unarmoured forms. Again, these apply well to the likes of King Bulbin, and to some other more powerful mook level opponents, but they're practically designed for the one enemy of that type to really return from Ocarina of Time: Darknuts.

He makes sure to hammer all three of those techniques in, before moving back onto more general and frankly, less complex, techniques (the first two were the Ending Blow and the Shield Bash) and the last two are the Jump Strike and the Great Spin - ideal for dealing with large numbers of lesser enemies.

In other words, not only is he dead-set on training his descendant in his skills and making sure masters them, but he really, REALLY seems to have a thing about heavily armoured, sword-wielding enemies and teaching his descendant how best to protect himself from them, so he'll have maximum practice before finally facing them. Like, say, Darknuts.

    Concerning Ganondorf 
How did Ganondorf suddenly obtain the Triforce of Power? Well...
When Zelda sent Link back to the past at the end of Ocarina of Time, the Triforce of Courage was split from him and remained in the future. However, upon returning to the past, Link still had his status as "chosen one of the Triforce of Courage". Since we know the Triforce is an inanimate object that cannot judge a situation on its own, the sudden appearance of a chosen one made the Triforce think it had become activated. However, just like when Ganondorf had tried to seize it, only the Triforce of Courage went to Link, the other two going to Zelda and Ganondorf, the latter not realising he even had it until he was mortally wounded.
  • This was confirmed as far back as Ocarina of Time itself; at the end of the game, you can see the Triforce of Courage on his hand in the final shot.

Ganon is Midna's father
Midna's Imp form looks a lot like Ganon from The Legend of Zelda: Ocarina of Time. Midna states that the Twili are descended from prisoners sent to the Twilight Realm, or whatever. Ganon was sent to the Twilight Realm and he is never shown attacking Midna. In the end of the game, he never hurt her, just pretended to, knowing Zelda and Link would turn on Midna. He also didn't grant Zant full powers (which it seems he'd be capable of!), because he suspected he might attempt to usurp her. Ganon is certainly powerful enough to establish himself as leader/king of the Twili, making Midna princess. Of course, for this to work, Midna wouldn't know Ganon is her father.
  • Debunked. Midna is the daughter of the last Twilight King.

Ganondorf dies at the end because at that same time Ganondorf summoned the Triforce in The Wind Waker.
The reason the Triforce leaves Ganondorf at the end of Twilight Princess is that he simultaneously summoned it in the Alternate Timeline, The Wind Waker. Thus, Ganondorf was truly ended by his own hand. The King then returns it to the Sacred Realm by wishing his Hyrule away and Link ends Ganondorf in The Wind Waker.
  • This actually fits with my theory that: Wind Waker Ganondorf's seal was broken because Twilight Princess's Ganondorf's seal was forcibly broken. And in turn: The seal used in OoT actually sealed both the past and present Ganondorfs away and by effect causing the split timeline.
  • Wouldn't Wind Waker Ganondorf have had the Triforce all along, though? He wouldn't have needed to "summon" it per se if he already had it.
    • The OP seems to be referring more to the moment when the Triforce is reunited at the end. At that point, the various Triforces scattered across the Multiverse would reconcile and leave a single Triforce.
      • In that case, it's debunked, because the Triforce has appeeared in its complete state in two separate timelines, which would be impossible if uniting it in one banishes the separate pieces from all the others.

Ganondorf didn't actually die in the end of the game
The one time we've seen Ganondorf properly die (at the end of Wind Waker), it was when the Triforce had already been used, and therefore Ganondorf didn't have it on death.This doesn't happen in Twilight Princess.
  • Jossed. Four Swords Adventures, the next game chronologically, features his reincarnation.

Ganondorf's initial execution was successful, but allowed him to become much worse than before.
Ganondorf has been established by the ending of Skyward Sword to be the bearer of Demise's rage, the curse laid against Link and Zelda for eternity. Ganondorf's exact relationship with Demise remains ambiguous, but it is possible in the Child Timeline, Ganondorf was killed by the Sages, but restored to life by Demise's curse, becoming a more direct vessel for his rage and gaining his immense power despite never laying hands on the Triforce in this timeline. Wind Waker Ganondorf wielded the Triforce of Power to attain a level of being beyond Demise's curse, which is why we see more of his motivation as the troubled but ruthless King of the Gerudo, but in the Child Timeline, Ganondorf became a full vessel for Demise's wrath after his initial death, which would explain why TP Ganondorf has the most similar demeanor and motive to Demise of Ganon's many incarnations.
  • Debunked. The game tells you he survived due to receiving the Triforce of Power.

When Ganondorf was killed, he sealed his spirit in the Trident of Power.
Vaati foolishly stole it to try to gain power, then when he was defeated by the four Links, Ganon used his body and/or soul to reincarnate.

Ganondorf's complexion
It's stated that something about the Realm of Twilight changed the ancestors of the Twili. It made them gentle, docile, and took away their anger. If Lanayru's representing them with Dark Link in his little history lesson is any indication, the Dark Interlopers may have also been more humanoid before the Twilight altered them. In this game, Ganondorf's skin has an almost blueish-black or greenish-black color. Not unlike some of the colors seen on Twili skintones. The magic of the Twilight could have been slowly taking hold on him, and may have turned him into a Twili if given enough time. Maybe it would have already done so if he hadn't had his Triforce to protect him.
  • Debunked. Ganondorf has always had greenish-bluish-blackish skin.

Ganondorf was reinforcing Zant's mind
Prior to the battle at the Twilit Palace, Zant is calm and collected to the point of eeriness. Once confronted, his Sanity Slippage quickly has him raging like a petulant child; the flashback to his initial meeting with Ganondorf shows him similarly unhinged. It seems that, in addition to granting raw magical power, Ganondorf made Zant into a more fitting tool by calming his moods and helping him think more clearly. Once Ganondorf has ensconced himself in Hyrule Castle, doesn't have much use for Zant and lets this mental buttressing fade away.
  • Potentially Jossed by Hyrule Warriors. Zant's profile says he like to act calm and in control, but quickly loses it when things don't go his way. His scenes and even fighting style in the game reflect that as well.

    Concerning the Twili and the Twilight Realm 
The Twili's culture involves suppressing their emotions.
During Zant's rant when he's encountered in the Twilight Realm, he states that the other Twili didn't have the "bloom of desire" and that they were content to stay in the darkness. Based on how crazy Zant suddenly starts acting in this final battle, maybe the real reason the royal Twili family didn't trust him (besides the fact that he wasn't in the royal line) is because he was way too emotional. He lacked the ability to stay level-headed in times of struggle, as we can see, and just wouldn't make a good leader. However, Midna is still fairly emotional herself, so that's a bit of a hole in this theory.
  • I think Zant was more upset about the other Twili's lack of ambition rather than emotion. He hated that they didn't want to take control of their destinies, escape the Twilight Realm, and get revenge on the light-dwellers who banished them there. So this theory is true in some sense.

Veran was a Twili
Hey, she looks kinda like one. Twinrova summoned her to defeat Link, because they really don't learn.
  • There'd be nothing "to learn", since TP is on the Child timeline, and the Oracle games are on the Decline timeline. This would also support the theory, because in the Decline timeline, Ganondorf is never exiled to the Twilight Realm, Zant is never granted his power, the Twili never invade, and Midna never shatters the Mirror. So Veran could definitely be a Twili summoned by Twinrova in the Decline timeline.
  • She also assumes the form of a shadow, the way Midna was shown to. But this would require an explanation for how she survives in the light when the only ones who were able to were protected by the Triforce.

The Twili were once Sheikah
"But wait! Weren't they the Royal Family's Protectors?!" The Sheikah are heavily stated to thrive on dark magic. Who's to say that they didn't get Drunk on the Dark Side? Those that were self controlled enough could resist the lure. Not to mention they guarding this family who have connections to this "Golden Power."
  • Some of the markings on the Twili's robes and on the walls you get pulled into are reminiscent of Sheikah designs. At least I thought so.
  • Some of they maybe the Dark Interlopers were most likely an organization that included many races
  • I recall reading that the tear in the Sheikah symbol is to commemorate a great betrayal. Perhaps that event was the rise of the Dark Interlopers, which also could have contributed to the Sheikah's dwindling numbers if enough of them broke away from the tribe and/or were sealed away in the Twilight Realm.
  • And they were corrupted by the dark energy released when Majora's Mask was destroyed.

The Twilight Realm consists of more than just the Palace.
Doesn't it seem odd that there were only 5 Twili left other than Midna and Zant? At that point in the game, you had only fought roughly 2 or 3 dozen Shadow Beasts, and I'd imagine that there would be a larger population of Twili over Lord knows how many years since whenever the Interlopers were banished. Also, Midna refers to her "tribe" multiple times, which seems to indicate a sort-of dark ages-style feudal governmental system in the Twilight Realm. So where, you might ask, are the rest of the Twili? There are other floating islands off somewhere in that void, which must be traverse through teleportation or slightly more conventional means, such as airships. (I'm thinking along the lines of Skies of Arcadia here.) Also, when she refers to Zant turning all of the Twili into Shadow Beasts, it could've been hyperbole, meant to emphasize the atrocity of what he was committing, or general unknowingness of the fates of the other tribes of Twili.
  • During some of Midna's flashback cutscenes, shots of solid ground were shown in the Twilight Realm, so Link's assault on the Palace of Twilight was basically a targeted strike, much like visiting the Temple of Time's past or going under the sea in The Wind Waker.
  • Even in-game, you can see other structures and buildings elsewhere in the realm. Of course there'd be more to it than what is explored in-game.

There are other ways between Hyrule and the Twilight Realm besides the Mirror of Twilight.
Think about it: if the Mirror of Twilight had been shattered, and that was the only way to get between the two realms, how did the Shadow Beasts get dropped into the areas where you fight them and why were the portals a different color? Were they being kept in a pen somewhere? It also doesn't really explain how Zant got from Hyrule in the Arbiter's Grounds and resurrecting the boss of that dungeon to being in the Palace of Twilight before you go there yourself.
  • It's probable that there were still Shadow Beasts in Hyrule (Hyrule Castle, perhaps, if not elsewhere), and we're never told when specifically Zant destroyed the mirror. It's entirely plausible that he reanimated Stallord, then warped outside and destroyed the mirror upon his return to the Twilight Realm.

Majora's Mask was made by the Twili
A tribe, using black magic made it, eh? And it's behaving a LOT like Zant. Oh, and don't forget that OTHER artefact of doom, which Link and Midna had to reassemble, which was said to be just as dangerous and had pretty similar markings to the Majoras Mask on it.
  • Except this implies that the Twili made the Fused Shadow. The way Midna speaks about it seems to indicate that it's older than they are.
    • Of course it is! Didn't you read the part about The Twili being descendants of the makers? They weren't Twili yet!
  • Not only are the markings similar, the Twili seem obsessed with masks in general. So much so that Midna wears Link's shield on her face when trying to figure out how human weapons work (and, yes, Midna even implies at the time that she thinks the shield is a weapon). This implies that the Twili think of masks as weapons and essential battle gear. As such, if they were to make some ultimate weapon, they would make a mask... IE Majora's mask.
  • Alternate thought: Majora's Mask WAS made by the Twili...but not the ones we met. Instead, it was made by the alternate Twili from Termina.
  • During the Lanayru cutscene, we see what was supposedly a Twili ancestor make Link disappear and then transform into him. Wait, so they killed people (or took their souls) and transformed into them? Like Majora took the Deku Butler's son's soul and turned Link into a Deku Scrub at the start of MM? Like Link, in a less evil way, laid Darmani and Mikau to rest and gained their masks so he, too, could transform? ...Well, fuck. Of course, the Twili ancestor in question looked like Dark Link, so that brings him into this.

The Fused Shadows either are Majora's Mask, or the Fused Shadows were an attempt to rebuild Majora's Mask
To take the above theory to a further level, consider the tale of Majora's Mask; a "mask salesman" traveling with an apocalyptic mask full of black magic... to where? Surely to destroy the thing, no? Nope. I'd be willing to bet that he was a member of the "tribe" who built it... and was bringing a prototype to the rest of them. Of course, things didn't go as planned, and the original Mask was damaged... so, after OoT/MM Link left Termina, the Happy Mask Salesman brought back what was left of the Mask, and the tribe rebuilt it... maybe giving it a new paint job and then some? Or perhaps finishing it? Unfortunately for the tribe, they were defeated by the light spirits, and the rest, as they say, is history.

For proof, there is, of course, the similar markings, the similar purpose, and the similar backstories of the Shadows and the Mask. Also, compare Majora's Wrath to the monstrosity Midna turns into when she wears the Fused Shadows; similar in the tentacle-like body composition and ferocity, but Midna's monster form is clearly much more horrific and powerful... as if the power of Majora was taken up to eleven. Furthermore, note that Midna and the HMS have similar demeanors, tactics, and general eeriness about them. If Midna is a descendant of the tribe banished to the Twilight Realm, and subsequently one of the makers of the Fused Shadows, which member, exactly, is her particular ancestor? Perhaps we've met him... which means... wait...

The passageway that Link and Midna use to get out of Hyrule Castle's dungeon in this game is the same one that will later be used by Link and Zelda in A Link to the Past.
  • Quasi-Jossed, going by the split in timelines. TP takes place on the Child timeline, so this Hyrule Castle is most likely the same Hyrule Castle in OoT's child era. In the adult era, where the Decline timeline branches off from, that Hyrule Castle has already been destroyed. The Hyrule Castle in ALTTP would therefore have to have been built during/after the Imprisoning War, where the victorious Ganon was sealed in the Sacred Realm with his Triforce. However, it is entirely possible that this is the same corridor in spirit, as the Royal Family could always instruct their architects to recreate it whenever they rebuild Hyrule Castle.

    Concerning the Oocca 
The Oocca are what occur when person/bird love goes too far in Skyloft.
Just to make an already disturbing race more disturbing. Somehow someway probably better left unexplored, the Oocca are the descendants of Skyloftians and their loftwings who refused to go to the surface and build the new kingdom of Hyrule.

The Oocca aren't actually an advanced race of pre-Hylians.
There was once such a race long ago, but they're dead now. The Ooccoo are just pets or experiments kept by the original Precursors, who were left behind when their owners died off. After which, the Oocca decided to squat their abandoned flying temple as their own while claiming that they were the original Precursors all along. This would explain why their 'city' looks absolutely nothing like a city at all, why everything there is apparently designed with much different beings in mind (including the contents of the one and only store — Link is actually only buying the remains of the temple's storage), and why everything there is in such an advanced state of decay. It also explains why Ooccoo (the one Occa to follow Link throughout the game) conveniently 'forgot' all the relevant details in how to return: Having been born there, and ignorant of how her home actually worked, she'd never known how to get back up in the first place. And so she started living in pots.
  • I'd say this is actually confirmed in Skyward Sword.
    • Building on that, possibly the Oocca are the evolved descendants of the Skyloft birds. Once humanity returned to the surface, the birds stayed behind, grew smaller due to no longer needing to transport humans, and... developed speech(?). Also maybe as the generations passed and the Oocca's general intelligence increased, since it's unlikely the birds had cognitive thought at first, their history/memories/etc grew hazier and their connection to humanity was skewed. If anything, the Skyloft birds certainly share the Oocca's bug-eyes.
  • The Oocca shopkeeper complains about having ordered items the Oocca can't use, but that in turn raises the question of how the shipments got to the sky. So maybe she was lying about that.

The Oocca were a prototype life-form made by the Goddesses
We know from the various mistakes that They are fallible, and that They made all life — creationism, not evolution. Thus, if they are fallible, but we have a "predecessor", both the seeming inconsistency and the Nightmare Fuel-esque nature of the Oocca are explained by them being a failed first try, who eventually were granted the Sky Palace as an apology for, well, being. It was still made for humans, of course, but given to them later on either when they complained or as a gift from the Sky People when they migrated downward and felt like making a nature preserve for the horrible atrocities against all that is right with the world.

The Oocca were something the Goddesses came up with after a night of binge-drinking and messing around with the Spore creature generator
Nuff said.
  • Alternate suggestion: The Occca were created by the goddesses on a dare, or perhaps as a prank gone wrong...very wrong.
    • The goddesses made a few of these horrifying creatures to scare someone. But they reproduced...very...very...fast.

The Oocca didn't create the Hylians or Hyrule, they created the Cucco.
I heard this one somewhere. Sounds plausible enough.

The Oocca are an alternate form of the Kokiri.
After the Great Deku tree died, they were incapable of preventing part or all of the forest from being clear-cut to create Ordon Village. They then abandoned the forest in shame and took on new forms to hide their failure.

The Oocca really are the "creators" of the Hylians
Thing is, they weren't always horrifying chicken things. The Oocca were what the inhabitants of Skyloft and other parts of the sky were originally humans like the Hylians, but opted to stay in the sky after access to Hyrule was reestablished. They're considered the "creators" of the Hylians in the same way that the British could be considered the "creators" of Australians in real-life. As to their appearance, at some point they were attacked by a powerful magical being who cursed them and transformed them into their current shapes, kind of like what Ursula does to various merfolk in the Disney version of The Little Mermaid, hence why the City in the Sky is clearly built for humans but populated by Oocca. At least some of the monsters in the City in the Sky used to be in Oocca zoos or were pets while others are basically invasive species, namely the plant-based monsters.

The Oocca are squatters in Zonai ruins
The supposed "Oocca technology" found in Twilight Princess like the Dominion Rod, its associated statues, and the whole City in the Sky are actually Zonai technology, with the Oocca merely being a sky-dwelling race that has managed to take over these abandoned Zonai buildings and use some of their technology for their own (and given the disrepair the City in the Sky is in, they can't fully understand Zonai tech).

    Concerning Other Characters 
The Skull Kid in Twilight Princess is actually the Hero of Time
It sounds ridiculous at first, but let's observe the following details. Firstly, he knows and plays Saria's song. This is nothing special, as Saria herself knows the song, as well as the Skull Kid that you befriend in both OoT/MM. What's intriguing, however, is he knows Zelda's Lullaby as well, as he appears immediately after you play the song on the howling stone in the Sacred Grove. It's also the only howling stone that doesn't summon the Hero's Shade. What's more interesting, is that this particular howling stone's design differs from the others; it does not have a Sheikah eye but a Triforce marking carved into it, with some very faint, scratchy depictions of OoT's Spiritual Stones etched into each Triforce Piece.

Secondly, we are led to believe that he is just playing dangerous games of hide and seek with us for his enjoyment. However, if you chat with Midna during your search, she makes it clear that he's not "playing" with you, but that he's actually trying to lead you somewhere. Further implying that he's actually guarding the ruins to the Temple of TIME, as well as the Master Sword; testing TP Link's strength and wit to see if he's worthy of becoming the next Hero in line.

In terms of looks, he's very different from the skull kids seen in OoT and MM; having a body made of flesh and bone rather then wood and straw, further implying that this Skull Kid is "different" from the others. He also has Hylian ears, and on those ears are a double pair of blue earrings - an accessory that's often associated with Link — the Hero of Time in particular. The base of his straw hat is long and an cylinder-shaped: much like Link's, but with a curve at the end of it's tip. The size and shape of the leaf on his back share's similar proportions to the Hylian and Hero's Shields that Link carried when he's a child in OoT. His lantern emits an eerie glow that's reminiscent to Navi's faded blue color. And lastly, he carries and plays his trumpet in his LEFT hand, it's notes and pitch sounding exactly like the Awakening Pipes that Link used in his Deku Scrub form in MM.

OoT heavily implies that people who become lost in the Lost Woods eventually turn into monsters. A Kokiri girl known as Fado says that adults turn into Stalfos, claiming that she had seen Grog transform into one during the Biggoron Quest. The Potion Shop Keeper who tried to save Grog comments that "this potion will not work on a monster..." A gossip stone implies that non-fairy folk (non-Kokiri) turn into monsters. Navi states that children who become lost in the woods eventually turn into Skull Kids. At the end of MM, we see Link — who is a child at this point in time - return to The Lost Woods after saving Termina. He is without a fairy and his existence fades into complete obscurity; never to be heard of again. Is it possible that the Hero's Shade was actually a red herring, and that he in fact became a Skull Kid, who felt obliged to guard the Master Sword for the remainder of his now-immortal existence? After all, it seems strange for a skull kid - of all things - to protect such an important place, let alone have some sort of connection with The Royal Family of Hyrule...

  • This is debunked by Hyrule Historia. Not only is the Hero's Shade the spirit of the Hero of Time, but the Hero of Time is the ancestor of the Link you play as in this game. He couldn't have sired a descendant if he were at the age the Skull Kid were supposed to be.

The Skull Kid from Twilight Princess is the same one from Ocarina of Time/Majora's Mask
That he knows how to play Saria's Song, which Link taught to the Skull Kid in OoT, seems to be proof enough. This is made even more plausible by the fact that TP apparently takes place in the same "Hyrule survives" timeline created by MM. Also, he appears in the Sacred Grove, an area that bears a conspicuous resemblance to the Lost Woods (in both background music and terrain), where the original Skull Kid lived. It's even possible that he was drawn to TP's Link because he reminded him of the old Link.
  • Supporting this is the fact that the grandmother's tale implies that said Skull Kid predates the creation of Termina by the four giants, meaning that he's immortal (given that he's a playmate of the local creator deities, one wonders why the witches describe pre-Majora's Mask Skull Kid as a harmless little punk.)
    • Immortality does not equate to power. Just 'cos he doesn't die and hangs with gods doesn't mean he's as powerful as one.
      • The WMG doesn't necessarily say anything about the Majora's Mask Skull Kid being powerful, just that, because he's immortal, it's possible that he could be around during TP.
  • This would be kind of fitting, given how he's been in two games already. Given how he knows the Hero of Time and all, it seems kind of fitting that he'd want / be able to guard the area around the Temple of Time.
    • This leads to another heartwarming angle. Consider how you first summon the Skull Kid using a Howling Stone, the same method as the Hero's Shade. It's possible that the Skull Kid truly considered the Hero of Time to be his friend, and continued to visit him for the rest of his life... and even after that...

The Skull Kid is actually Saria
It can play Saria's song because it invented it, also note that it forces you to run its little course once to get the Master Sword and again to access the Temple of Time. It isn't just messing with you, she's trying to protect the Master Sword in the first instance and test this Link's skills the other time. Being close to the forest temple and still alive (they never age) it could feasably work out.
  • Debunked from in-game dialogue. The Skull Kid looks and is referred to as being male.

The monkeys are an alternate form of the Kokiri.
After humans invaded and took over their beloved woods and killed their Deku Tree, they were forced to take a new form. That female monkey is Saria and Mido is Ook. They are triggered in reaction to Link by their old memories. Speaking of Links, I can see OoT Link dying while trying to help them protect the forest, who didn't recognize him, putting a new spin on the female monkey's "green-clad prince who helped me" remark. (Yes I do believe that OoT Link and Zelda are related.) And if the below WMG is too be believed, it explains why he was there.
  • The female monkey can't be Saria because Saria is a sage. And Kokiri aren't immortal. I don't know if they die of old age (they don't grow up, but everything gets older), but we know of at least one, possible two (Wind Waker Fado for sure, and Saria if you believe that the sages died) who are dead. I'd say that, while it's possible that the monkeys, like the Korok, are descended from the Kokiri, it's unlikely that there are any Kokiri we know among the monkeys.
    • Saria didn't become a Sage in the childhood timeline, which TP follows, but I agree with everything else. Monkeys are monkeys and Kokiri are Kokiri.
    • Alternately, Saria was manifesting as a monkey in the same way that Rauru manifested as Kaepora Gaebora.
    • It's still possible the monkeys are descended from the Kokiri. The Koroks in Wind Waker are all but stated to be Kokiri and Skyward Sword gives us the Kikwi, who are also tiny forest-dwellers, and possibly the precursors to the Kokiri. If the Kokiri can be bound to faries and look young foerever, then change into tree-people, who's to say they can't change into monkeys in a different timeline?

The Ordonians are descendants of the Kokiri
When the Great Deku tree bit it, they became like ordinary Hylians, eventually grew up, and had chldren, who had children, etc. It might seem strange, but there was never any clarification over whether the "Kokiri die when they leave the forest tale" was literal, or a more metaphorical slow death through aging. Also, in the ending of The Legend of Zelda: Ocarina of Time, we see them outside the forest. Why? Because the Deku Sprout told them the truth. They are eternally children as long as they stay in the forest, but losing that protection by leaving (or their guardian dying) nullifies it.
  • According to The Wind Waker and Breath of the Wild, it's suggested that the Kokiri are guaranteed to turn into Koroks whenever they leave the forest. Debunked.

The Kokiri are dead.
  • This game takes place in the Child timeline split. In the Adult timeline split, the Hero of Time cleared through the cursed Forest Temple, destroying Phantom Ganon, and allowing a new Deku Sprout to be planted, which we see as a fully grown Deku Tree in Wind Waker, who had protected the Kokiri, and turned them into the Koroks. In the Child timeline split, the Forest Temple was never cleared (Ganondorf could have corrupted the temple at the same time he cursed the Deku Tree, sealed Dodongo Cavern, and made Jabu-Jabu sick, perhaps knowing about the Sages protecting the Triforce/Being a force which could actually stop him, as they did in the defeat timeline split), since Link never needed to, as Ganondorf was already defeated. At that time he went into the Lost Woods searching for Navi, and Majora's Mask happened. After that, something happened to the Hero of Time, whether he became a Stalfos, stayed in Termina, or went back to Hyrule and settled down with, say, Malon. Since the new Deku Sprout was never planted, the Kokiri lost their guardian spirit, and either faded from existence (if they were simply sprites created by the will of the Deku Tree), or were helpless, and eventually died off. We never see the Kokiri, nor the Deku Tree, again in this timeline split, even though the Lost Woods feature very prominently in Twilight Princess.

Aryll and Ilia are counterparts of each other.
Their roles and personalities are almost the same and they have pretty much the same age difference to Link. Since we don't know who Link's parents are, Ilia could, in theory, even be his little sister (or half-sister), just like Aryll. They are also both associated with animals (Seagulls for Aryll and Horses for Ilia), both have their own Leitmotif and are both blonde. Also, look at the 2 Link's faces, when they "talk" to Aryll or Ilia in cutscenes. They have this special "I'm so happy to see you today" look in their eyes, which differs greatly from their usual, heroic expressions. Both Links only have this look in their faces when they see Ilia or Aryll, on no other occasion.
  • That "I'm so happy to see you today" look is because Aryll and Ilia are both people their respective Links care a lot about. What does that have to do with them being related?

Stallord is Volvagia revived by Zant
They share a very similar build, right down to the head shape and hair. Plus, Volvagia was skeletonized at defeat.
  • Stallord uses Volvagia's boss theme in the last phase, as well. Of course, this theme is also used by King Dodongo, so that's another potential theory.
  • No, they do not have a similar build. Stallord has a ribcage, suggesting he had a chest cavity whereas Volvagia was a serpentine dragon whose head dwarfed the Hero of Time in size.

Zant is an evil Wizzrobe, Midna and the Twili are good/lawful neutral Wizzrobes.
Zant has all the same powers as the Wizzrobe race (magical energy weapon, teleportation, apparent levitation). Midna, too, shares all these similar powers. Even looking at Zant's helmet, with its weird googly eyes and pointy head, suggests a Wizzrobe. Not enough? Look at the arms of his robe, and notice that they match identically to the Toucan-Sam-Wizzrobes of [[Wind Waker]].
  • Debunked. Zant's only power comes from Ganondorf, whereas Midna's comes from her bloodline or the Fused Shadows.

Queen Rutela will become the new Sage of Water
The evidence fits together. The sages in Ocarina of Time didn't truly awaken until after their untimely deaths. There's a definite gap in the roster after Ganondorf's pre-sealing rampage, and the existence of seven sages (counting Zelda) is a common element of the series as a whole, meaning they'll need a new one sooner or later. She's still around in a ghostly form, so clearly her role in the story isn't over yet. And most noticeably, all of the sages that appear in this game have taken a humanlike form since their inception, and Rutela's ghost looks considerably more like a human than most Zoras. She must have already started the transformation...
  • Debunked, because Rutela is already dead by the end of the game, and The Wind Waker tells us that ghosts and spirits can't act as sages.

Malo is a midget.
We only think he's a child because of the game's weird art style. He is actually an old and retired warrior (who just happens to be a midget), who was a legend in his own time. He already knows everything about swordplay (pay attention to his dialogue during the tutorial), and if you try to hit him with your sword, he dodges like Neo dodges bullets. The fact that he successfully opens up a chain of retail stores also shows that he is much more intelligent than any toddler. His cynical, sarcastic attitude is a result of his long, gruesome war campaigns. So yah, Malo is a midget. A badass midget.
  • Jossed by the supplemental material. According to Word of God, Malo is four years old.

Renado is a Sheikah.
They don't all have to be exceptionally obvious about it, though the symbol on his robe is rather suspicious.

Navi died in (or at the very least never made it out of) the Temple of Time.
The logic behind this comes from looking at both TP and OoT. Navi flies off through a window; the same window that leads into the secret entrance to the Temple from TP. You know, the one full of monsters, confusing puzzles, and elaborate death traps.
  • And how does that factor into Navi dying from any of that stuff? Considering what an adventure she'd gone on with Link, it's not as if she'd have significant trouble avoiding any of it.

The scene in Hyrule Castle with the Resistance members coming to Link's "rescue" wasn't Cutscene Incompetence.
Link was perfectly capable of handling all those opponents, and they were fully aware of this fact. It was simply their way of saying "we got your back", and they figured they would say it with style.

Colin is the future incarnation of Link.
He is the bravest of the kids, he wears clothing similar to Link before he wore his hero garb. He also has the same hair and eye color of Link. Not to mention he admires the hell out of him. Lastly, he is seen in the final cutscene with a wooden shield similar to Links first shield.

The Yeti are naturally hairless.
If you look closely at their "fur," it has a mix of nonsensical patterns, textures, and growth-directions. It also ends abruptly with no hairs visibly growing out of the skin. The skin we do see is scaly, I think they're just reptilian humanoids that wear a bunch of animal furs. Matonya/Yeta is clearly just wearing an armless sweater.
  • Debunked. The costume that Ashei wears when you meet her at Snowpeak is referred to as a "yeti's pelt".

Female Yeti have two faces: one for social appeal and one for battle.
Ever notice how, when Yeta becomes Blizzeta, her entire head swivels around within her pelt? This implies that she actually has two faces — while this could be explained as an effect of the Mirror of Twilight, it's also possible that it's a natural defense mechanism meant to scare off predators. I mean, just look at the male Yeto - he's got large eyes and green skin, just like Blizzeta does. Maybe there's a correlation there (although Blizzeta's cryokinesis was definitely a part of the Mirror's effects).

Telma is a Gerudo.
  • Telma's physical appearance, with the red hair and darker skin tone than Hylians. It's possible that in this timeline, with Ganondorf sealed away by the sages, Nabooru took command of the Gerudo and integrated them into Hylian society. Telma is likely a Gerudo-Hylian hybrid, as Gerudo women are known to take Hylian or Human boyfriends.

Ilia is a descendant of Malon
It makes sense when you think about it. Both of them are young girls/women who grew up on or near a ranch, both are close to Link in a platonic way at the very least, both are great with animals - namely horses - and both have short tempers (though Malon's is more implied by her father than anything else). And another piece of evidence for this theory is that Ilia's theme has the distinct sound of Epona's song mixed into it. Sure, you could make the argument that it's just because she cares about Epona, but it's still something to point out seeing as how Malon was the one who originally sang and taught the song to Link! And even though Ilia doesn't have any musical abilities (as evidenced by the fact she has difficulty playing the horse whistle grass and that we never hear her sing, unlike what happens with Malon), that is almost completely irrelevant seeing as how not all traits - whether physically or personality-wise - are passed on between ancestors and descendants. Genetics just don't work that way.

    Concerning Other Things 
The Snowpeak Ruins used to belong to a noble Hylian family.
Think about it, why is it there? It does not belong to the Yetis originally. Also, why is there only one Hylian in Ordon? A teen boy no less. Also horses appear to be rare and only belonging to people of well standing. What if as this Link is a descendant of OoT!Link, and since OoT!Link, maybe his family became nobles? But OoT!Link felt bad about living in a big city (trauma from Majora's Mask), so he and his family moved to Snowpeak. They lived there happily, lived of hunting, fishing and gathering. OoT!Epona possibly had children of her own too... and one day little TP!Link is born. Brings big happiness etc etc. But Ganondorf wants revenge! The royal family notices this, but the mailman is late (from being cold, losing the letter in water, accidentally burning it etc). And when they finally get it, they know that they have no time, and sets little Link one of their (pregnant) horses, TP!Epona's mother. She runs off and to the end of the country. Link's whole family is slain, and TP!Epona is born a while later, but due to all the stress and pain her mother dies some years later. That way TP!Link got to Ordon.

The Snowpeak Ruins is all that's left of a long-since-forgotten attempt to invade Hyrule.
Consider the setting: it's high in the mountains, surrounded by ravines and nearly impenetrable (thus easily defensible), so it's an excellent forward base for whatever army was planning to take over Hyrule. The only path into Hyrule leads to the Zora River, which could be taken to prevent any attacks from the rear, and is still a nearly unassailable position from which to attack the castle or the lake. The various paintings that can be found depict scenes from around Hyrule such as Ordon Ranch and the Arbiter's Grounds, again to prepare the invasion. Not to mention all the ancient weaponry on the walls, as well as the cannons.
Now for the long-ago part: the ruins are filled with weapons, which were probably used to train new soldiers. When they died for reasons unknown, their raging spirits bound themselves to the ice and wind, becoming the Chilfos, who retain a goose-stepping walk from their military training. The Darkhammer miniboss is either the result of magical experiments to create an army of Lizard Folk, the weaker of which populate the warmer climates or of the surviving soldiers inbreeding to the point of becoming thick-skinned animalistic monsters. In either case, they retained the use of simple (beat it til' it breaks or slash it til' it dies) weaponry by mimicking their elders, even when all semblance to human language had been lost, which is why the cannons are in disuse.
  • How long? The monsters were said to have only shown up recently.
    • Because now they have sufficient numbers, they were all in hiding/hibernating before.
    • Plausibly the monsters were riled up by Ganon's influence. It's happened before.
  • Why does the Dark Hammer have to be anything other than a lizard to begin with? This is a universe where sentient creatures made of rock, and people whose heads look like fish are completely normal. The invaders' original species could've been lizard-like. Maybe the Dark Hammer is the Last of His Kind.
    • Or he's just an unusual Lizalfos.
  • This troper has always believed this exact same idea. Furthermore, the hidden cave in North Hyrule field decorated in the same style could be an outpost for spying on Hyrule.
  • Jossed in the manga: It's actually Ashei's family home, though it's fallen into disrepair.

The Faron and Ordona provinces are actually the OoT Hyrule.
Everyone assumes that this is the same Hyrule, unchanged from before. But a lot of things are too out of place to account for that. When you look at the position of these two provinces, and the Sacred Grove/Temple of time, it all adds up. Ordona is almost the exact same shape as Hyrule field from Ocarina of Time, and forest overgrowth could account for it being smaller (but only slightly. OoT's field was not that big and Ordona is pretty big, and is bigger when adding Faron to it). The Sacred Grove is Castle Town, and the Temple of Time is the exact same one from Ocarina of Time, location and all.

Due to the cracks in the field in Twilight Princess, one can easily infer that it is tectonically unstable. Couple this with a possible need for conquest further north (probably over taking some other country that was there) and we have Hyrule from Twilight Princess. I believe several locations remain the same, such as Death Mountain (which, being an active volcano, lends more credence to the theory) and the Gerudo Desert, except the tectonic shifts caused them to drift farther apart. I believe that, in OoT, when Link traveled to either location, there was a sort of unseen moment (probably during the brief loading areas) where he traveled quite a large distance, to get to the mountain or the desert.

I believe that this Lake Hylia is a new one. The old one possibly drying up could be another factor into the kingdom's movement northward.

The temple part of the Temple of Time is actually the Temple of Light we never get to see in OoT.
It makes sense. They never got to include said dungeon in OoT, so they included it in this game. "But it's called the Temple of Time" is not a good argument against this guess. Neither is "But you physically enter the Temple of Time, and the Temple of Light exists in a non-physical plane." because it is possible that the name is just Link or Midna guessing as to what it is, and that going up the staircase of light (ding ding, that has to set off some bells) and through the fake stained glass is a physical representation of entering a spiritual realm, in which the Temple of Light exists.

The strongest evidence is that everywhere you look, the Medallion of Light symbol is shown, and the fact that you enter it from the Temple of Time, which in OoT is said to be the only entrance to the Temple of Light.

The temple part of the Temple of Time is OoT Forest Temple in a cleansed and upgraded state.
If you believe in the theory about TP Forest Temple being the dead Deku Tree, then Temple of Time is the old Forest Temple in a cleansed state. It supposes that the Temple of Time and the Master Sword were moved to the Sacred Grove (the equivalent of Lost Woods in this game), before the Forest Temple to make sure it doesn't fall into malicious hands, and the coupled influence of the sword and the Grove transformed it into the Temple of Time.

The Lakebed Temple is a water purification plant.
Tying in with the "Hyrule is geologically unstable" and the "Faron and Ordon are Ocarina of Time Hyrule" theories, the Lakebed "temple" was actually a facility built by the Zora to flush massive impurities out of Hyrule's water so they could live in it. The source of those impurities being, naturally, some kind of massive eruption by Death Mountain plus earthquakes.
  • Morpheel's chamber was originally the area in the facility where the Zora population lived while they worked on detoxifying the rest of the water.

The Gorons skin Dodongos alive.
Dodongos explode when you kill them, but in at least Twilight Princess a Goron has what look to be dodongo skin hanging on their walls, so the Gornon must skin them alive, and the dodongo later explodes after bleeding out from lack of skin/scales.
  • Or they just wait for them to die of old age/exertion by rolling after them/blunt force trauma instead of sharp objects.
  • It doesn't even have to be anything that gruesome... Dodongos resemble giant lizards, who's to say they don't just shed them as they grow?

The Metroid series was leaking into this game.
Along with the theories about the magic armor being a prototype for Samus's suit and the City in the Sky being Sky Town, there are several other similarities that may or may not be intentional:
  • The Spinner has several similarities to the different Morph Ball abilities, mainly the boost ball and the spider ball. Boost Ball, in that it can attack much like the boost function, and it can insert itself into various different spinning powered devises that interact with the landscape, such as extending bridges; and the Spider Ball, in that it can quickly travel across specialized, often wall mounted rails, and can use the little spin boost function to jump between rails that are close enough.
  • The Iron Boots also have similarities to the Spider Ball, in that it can attach to magnetic surfaces to allow travel to new areas.
  • The Bomb Arrows are basically the closest thing to missiles the series can muster. They're even used to destroy stalactites to make platforms!
  • Diababa bares many similarities to Flaagrah, mainly being giant mutated plants that reside in poisoned water and must be defeated using bombs.
  • The fight against Stallord is similar to the fight against the Quadraxis, mostly in the second phase where the boss's disembodied head is flying around the center of the arena and must be attacked using the item that bares similarities to the Morph Ball.

The Magic Armor doesn't consume rupees, it sends them back to Malo Mart
That's why he can sell you the Magic Armor for so much less than the Chudley's asking price; he (potentially) makes up the difference by connecting the armor's protective magic to his own coffers.

Ordon is a fairly recent addition to Hyrule.
The only family with Hylian blood seems to be Link's, implying there hasn't been much interaction with the long-eared inhabitants of Hyrule proper just yet, and Link's initial task is to bring Rusl's sword "to Hyrule" as a tribute. On a map, Ordon is part of Hyrule, but that's such a new development that they think of themselves as Ordonians first and Hyruleans a distant second. They pay tribute to the monarchs but for the most part are left alone to do their own thing, since they're on the wrong side of the historically very hostile forest to do all that much trade. Taking something to Hyrule Castle Town and taking something to Hyrule are the same concept to them unless you're arguing semantics.

It's possible that Ordon itself is a fairly new settlement in general, and in this case it was probably settled by people travelling far from their original homeland. The Hero of Time probably have met them during his travels and settled down with them in the treehouse that the Hero of Twilight inherited.

The Darknuts are a race of giants who once served the royal family of Hyrule.
Throughout Hyrule Castle, ancient suits of armor can be found standing throughout the upper halls - however, these suits are much too large for a regular Hylian such as Link. It's possible that that armor was once used by some sort of benevolent race or bloodline of giants, but something happened and there was a falling out, leading to the giants siding with Ganondorf instead. Now their royal armor remains unused, ancestral heirlooms.

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