If you search around a bit in Link's room, you'll discover a few wooden carvings — a few in-progress meaning he is, in fact, making them. Now, what is Skyward Sword's core gimmick? Motion-controlled swordplay. In other words, precision cutting.
Unlike most other Zelda games involving time travel, you will never see all of the past version of the Lanayru region; therefore, you'll always be wondering what all the ancient structures looked like and how the inhabitants lived, thus adding to the desolate mood and atmosphere of this region.
A few examples pertain to Ghirahim and his true nature.
Also, his flamboyant behavior and tendency to describe how he's feeling foreshadows that he's Fi's opposite.
Remember Ghirahim's arm speech in the Fire Sanctuary? He wasn't just monologuing about his beauty, he was taunting Fi for her lack of arms!
A metallic sound effect is heard whenever Ghirahim does his magic, as well as when you land hits on him during boss fights.
His appearance resembles a fencing outfit (minus the mask), and he wields a saber in his second phase. What could be more appropriate for a sword-to-sword duel? It's also another hint at his connection to Fi, in that they both wear copious jewelry, clothes with diamond patterns, and capes.
Speaking of capes, Ghirahim makes it a point to shed his each time he prepares to spar with Link. Given what he really is, you could almost think of his cape as the sheath to a sword.
Ghirahim's appetite for rage, violence and bloodshed correlates to him being absorbed entirely into the blade of Demise's sword when summoned, which also symbolizes Demise's view of him as just a weapon and a tool. Comparatively, Fi is consistently stoic and logical because she's tied to the hilt of the Goddess Sword, through which Link is able to temper and control its output as a weapon — it's what she emerges from and retreats into when summoned, and when prompting Link to call on her, it's the only part of the sword that flashes. This also underlines the connection she forms with Link as opposed to Demise's indifference toward Ghirahim as a character, because the hilt is also the point of contact between a sword and its wielder.
If you Enemy Scan an Aracha, Fi tells you it's a larva that has a 1000-year life cycle and is constantly growing, which should clue you in to the idea that there's a giant one around somewhere.
The first time Zelda's Lullaby in this game is when Zelda actually puts herself into a long sleep, making it the first time it's been used as an actual lullaby.
The reason Link starts with six hearts instead of three like in all the other games is that he's gone through training at the Knight Academy, which buffed up his endurance.
Beedle complaining that Link is heavy. He may not seem to weigh much, but keep in mind he's carrying a sword, a shield, and all of his gear (yes, even the bugs and treasures).
Why does the lava in that one section of the Fire Sanctuary instantly kill you? Because Link isn't able to leap into the air and escape from certain death while underground.
All the structures and enemies in the past version of Lanayru Desert have this red-and-blue abstract pattern on certain segments. A similar red-and-blue motif can be found in Gerudo-related designs, though the Past-Lanayru patterns are typically gaudier than the more faded, deserty Gerudo patterns. This signifies how the Gerudo probably came across relics of the past (such as the robots or buildings) and decided to incorporate elements of those designs into their own. Cross-reference an Armos◊ with Ganondorf◊.
While it seems odd that the Master Sword earns its power from the Sacred Flames in this game rather than sage blessings like in The Wind Waker, two of the three flames actually grant the same blessings as the sages' prayers. The sword gets its sharp edge via Farore's Flame and the prayers of the Earth Sage, while its evil-repelling shine is granted by Din's Flame and the prayers of the Wind Sage. The dungeons where you earn both sets of blessings are also similar, the Ancient Cistern to the Earth Temple and the Fire Sanctuary to the Wind Temple. The icing on top is that the Master Sword's penultimate form is that of its depowered state in The Wind Waker.
Faron Province is associated with Farore, the Goddess of Courage. The dungeons of Faron are also where you find the vast majority of the game's undead creatures, which are pretty scary, and which require courage to face.
The Herald of Hyrule is a bird◊. Now we know where it comes from: Loftwings. Even better when one notices that the crest of Hyrule on the Hylian Shield has the bird in question colored red, making it match the Loftwing that was bonded to Link.
The two springs where Zelda has to purify herself are located, respectively, in the Skyview Temple and the Earth Temple. Why? They symbolize her descent from the sky to the earth, and the celestial being Hylia reincarnating into an earthly being. Itself is one giant puzzle, and solving it all proved that Link was truly worthy to claim that last piece.
According to the timeline released by Nintendo, this is the oldest game in the series (in-universe), followed by the second-oldest game in-universe, Minish Cap for the Gameboy Advance. In Minish Cap, there is an entire civilization and set of temples that exist above the clouds. Perhaps the remnants of the civilization from Skyward Sword?
Of the three Sacred Flames, Nayru's Flame is the only one that doesn't increase your sword's attack power. Instead, it increases your ability to gather information — appropriate for the Goddess of Wisdom.
When Fi thanks Link at the end of the game and hopes they'll meet in another lifetime, what do you suppose happened? What other character do we all know just like Fi? Navi! That's right — when Fi expressed her gratitude, Hylia realized that Fi, her creation, had become more than just a machine, and deserved more than an eternity in a sword! Reincarnation is a major theme of the game; it makes sense that Hylia would put her agent, Fi, in a place of such massive instability — namely, the period of time during which Ocarina of Time took place. That particular game was responsible for splitting the timeline into three pieces; Hylia sent Fi as Navi to help Link of the future! Who better to help a legendary hero than Fi, who already knew the legendary hero? It also helps that both Navi and Fi have similar sounding names, serve the same purpose in both games, and are both rather annoying when you ignore them.
This game was known to detail the origins of the Master Sword long before the game was released. But why was it named the Master Sword? This version of Link was the one who unlocked the hidden potential within the Goddess Sword, thus creating the Master Sword in the first place. Fi is the living spirit of the Goddess Sword. What does she call Link, the one who wields the sword? She calls Link her "master". The name "Master Sword" is a reference to the original owner of the blade. The very first "Master" of the sword is Link himself, thus making the "Master Sword" his sword! As shown by the ending, Fi treasured her time with Link despite it just being her purpose. It is brilliant (and also heartwarming) to see that the spirit within the sword named it after her very first companion. It is also a play on words. Assuming Fi is the one to introduce the next protectors to the sword, what would she call it? Master's Sword, which sounds exactly like...?
Lullaby:
It's well known that the Ballad of the Goddess is Zelda's Lullaby backwards; The Ballad of the Goddess backwards is, therefore, the goddess's lullaby.
The first time Zelda's Lullaby plays in this game is when Zelda actually puts herself into a long sleep, making it the first time Zelda's Lullaby has been used as an actual lullaby.
A pretty silly one: Fi is your sword. The game uses Wii MotionPlus to have 1:1 (-ish) sword motion — in other words, your Wiimote is your sword. Therefore, Fi is your Wiimote, and therefore she doesn't actuallybreak the fourth wall when she tells you your batteries are low — they're her batteries!
Fi's singing expression (and some of her other mannerisms) tend to be considered Unintentional Uncanny Valley territory by the fanbase. But this makes perfect sense when you consider that she is, essentially, a goddess-supplied helper-bot created for the sole purpose of aiding the hero and has had (to the best of our knowledge) next to no human contact prior to Link.
As you progress through the story, stronger enemies will pop up in each province. At first, this was put to the game just making things harder as the player gains experience. But when it is revealed Demise's seal is weakening, it means that his power is flowing into the enemies and making them stronger.
At the end of the game, it's revealed that Ganondorf is an avatar of Demise, while Zelda is an avatar of Hylia. That leaves Link as apparently a mere mortal. Or is he? He's someone's avatar... yours. The "Link" from our world to theirs.
Groose's character development from jerk to a pretty competent deuteragonist has some great foreshadowing: his outfit (and hair) is mostly made of the primary colors red, blue, and yellow, a scheme normally reserved for heroes.
He wears a necklace that has red and green beads, foreshadowing that he’ll turn to Link’s side in the end.
Another example concerns Groose's Loftwing, which you see is colored black when he rides it during the Wing Ceremony. This seems like just an easy way to indicate Groose is an unsavory character, and most players wouldn't think to look into it any further. But his Loftwing is also the same color as an inactive Goddess Crest. Symbolizing that Groose does have potential; he just hasn't been convinced to draw on it yet.
Of course drawing the Bug-Catching Net stops Demise in his tracks to stare at it. This is someone who had never before encountered anyone brave enough to stand before him and fight — and now this same person pulled out something that wasn't even a weapon. The Big Bad was staring at you in utter confusion!]
At the beginning of the game, Zelda acts very concerned about Link not being able to win the race and become a knight, with her father saying she's like a different person when she's worried about Link. Later on, it seems that it was Zelda's latent memories as Hylia driving her concern, with the goddess coming through in concern that Link couldn't be the legendary hero. Zelda really is a different person underneath, so her father was correct- her Hylia self is speaking during those moments, looking at Link's potential in the greater picture.
When Ghirahim sheds his gloves to fight Link in the Fire Sanctuary, the black marks running over his body almost resemble the kind of scarring that a lightning strike would leave you with. Link and Demise end up dueling each other by channeling lightning strikes into their swords, one of which turns out to be Ghirahim's true form.
During the final battle, lightning will tend to jump into Link's sword first despite that Demise appears to be the one calling it down. That's likely because the lightning is being channeled by their respective sword spirits. Fi would be quicker on the draw than Ghirahim since she's been using her Energy Absorption abilities to help Link all throughout the game, whereas Ghirahim only got around to it during the second phase of his last battle.
The Ballad of the Goddess' name is one. A ballad is a narrative poem/song, which usually tells a story. In game, the song is an ancient story whose lyrics both refer directly to Link, calling him "guided by the servant of the goddess", and actually guide him on his quest by telling him how to find the Sacred Flames; the Goddess it refers to is Hylia, who is revealed to have been reborn as this game's Zelda. That means the Ballad of the Goddess is an ancient story for and about both a hero and his adventures, and the one he serves, a goddess who reincarnated herself into mortal form as Zelda. That means you could call the Ballad of the Goddess... the Legend of Zelda.
Link starting with six hearts may be a stealth reference to the very first game, where players who knew where to look could have six hearts before stepping foot in the first dungeon.
Judging by the positions of the dead robots and Bokoblin skeletons you see in the Lanayru Desert, it seems that whatever burned out the region happened FAST. It could be a result of the Dragon Lanayru dying.
When you approach the bones of the Dragon Lanayru and "examine" them, there is still a faint light in his eyes. He says, when you heal him, that he has "eternal life." What if that means that a shred of him still survived, imprisoned in a dead and powerless body for the whole time up until Link finds him?
The subterranean area of Ancient Cistern was a mild case of Fridge Horror — after all, there have been plenty of creepy dungeons throughout the years. But think about it — the Hindu imagery, the golden light colors, the lotus blooms — it's pretty much Heaven. And what's downstairs from Heaven? That's right. Link just went into a zombie-infested, blood-watered Hell.
Skipper, like all of the little robots in the desert, is only alive in the past. And Skipper proved the robots are actually aware that they are in a future where they and everything they worked for has decayed and been forgotten. They may be robots, but they're sentient and have personalities. You'd think that'd create some sort of existential dread.
After Link defeats Tentalus, Skipper and his crew are now in power of the ship again. However, we find out earlier that Skipper has a wife and child living in Skipper's Retreat. (This can be assumed by reading the pieces of paper on the walls of Skipper's Retreat — one of which is a note from his child. There are two deactivated robots in the Retreat — we can assume they are his family.) Skipper has revealed that he cannot access his old home, which is why Link has to get the sea chart for him. He even laments how much he misses seeing his family if you visit the retreat later in the game.
Before his second fight, Ghirahim makes a speech about a "thread of fate" binding him and Link to do battle, and that he intends it to be "stained crimson with [Link's] blood." Creepy enough, but takes on another meaning if you're familiar with a certain Asian proverb. It says a lot about Ghirahim that this isn't the most blatant pass he makes at Link.
It's disturbing when considering how often Ghirahim mentions how young Link is, frequently referring to him as a child and once calling him a "mischievous boy" who needs to be punished. He considers Link to be a child, and has no problem with attempting to torture or murder him.
You know how if The Imprisoned gets to the top of the Sealed Temple, you get a Non-Standard Game Over? Well... it's because Zelda is inside the temple, locked in a thousand-year sleep, and completely defenseless. And you have no idea she's there the first couple of times you fight him.
In the opening cutscene introducing Skyloft, we see the Crimson Loftwing later revealed to be Link's. As the scene continues, you see Groose and his gang jump onto their Loftwings, trailing down your own. That's right, this is the scene where he kidnaps your bird.
Potions are improved by adding bugs to them. Think about that every time Link gulps down his Heart++ potion, which is upgraded via the Eldin Roller — a dung beetle.
The blade of Demise's sword has an upside-down Triforce on it, which happens to resemble the Triforce of Lorule in The Legend of Zelda: A Link Between Worlds. Notably, you never actually see Lorule's version of the Master Sword, leaving open the possibility that Demise's sword could be it. Ghirahim being Fi's Lorulean counterpart would fit the theme of juxtaposition between worlds.
Possible evidence of this is that A Link Between Worlds implies through Yuga's smug arrogance that Lorule's counterpart of Ganondorf is centered on the virtue of courage, rather than power. What if that did extend to Demise? He's remarkably confident in his own abilities, and most tellingly, he frequently commends Link for the tremendous courage the mortal boy displays in stepping up to face him in combat.
Related to this, the game introduces a set of three colored flames that are used to enhance the Master Sword into its true form. Invert the colors on those three flames, and you get one that's blue, one that's red, and one that's purple - the same color of the flames that were used to revive Ganon in the Oracle games. What if Demise used those flames to temper his sword similarly?
After telling Link that Zelda is alive in order to entice him to draw the Goddess Sword, Fi appears to study the effect the news has on him before concluding that "further persuasive measures" are no longer necessary to convince him. We're never told what further measures she had planned, but for someone with telepathy who can even appear in people's dreams as she desires, there's a lot of potential regarding what she might be able to do to influence him.
The very existence of Timeshift Crystals has some alarming implications, beyond what's presented in this game. They are apparently an ubiquitous mineral within the Lanayru region, and require only a sharp impact to activate their effects. The robotic civilization died out before they could exhaust this resource, meaning there are probably a lot more such crystals still buried beneath the area ... crystals, that might still be there underground, waiting for some random cave-in or injudicious miner to trigger them, in the eras of the other Zelda games. In Skyward Sword Lanayru is a desert populated only by monsters, so having a few of them vanish as bits of landscape are time-shifted isn't anything for Link to worry about. But in most other games, that same province is the seat of Hyrule's government, and home to a large fraction of its citizens. How many innocent people have been erased from Time without any warning, in the millennia since the desert became habitable again?
◊ with Ganondorf
