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    Chancellor boss 

  • How exactly was the Chancellor able to boss around both the guards and Princess Zelda? Isn't she the ruler? In one early level, you have to sneak her out from her own castle because he has her guards keeping her inside. How? They're pretty clearly not hypnotized, so shouldn't her authority overrule his?
    • Notice how she's the "princess" rather than "queen" despite the fact that her parents aren't even hinted at? That's not just for tradition. It means she's not been officially crowned yet, therefore she doesn't have her full authority. Until Zelda comes of age, she's basically regulated to ceremonial duties. Cole, as Chancellor and royal adviser, is the guy with all the practical power for the moment, which is why she couldn't directly act against him.
    • That's odd. Considering at the end she does the "paperwork"...
    • 1) Paperwork does not equate to actual authority to remove trusted officials. 2) This is after Cole is removed from power (and life). 3) She has Teacher alongside her.
    • Early in the game, though, there's a guard who complains about the chancellor being so big-headed and arrogant, but that Princess Zelda is 'so nice' that she pretty much lets him get away with it, implying that she could really do something if she wanted to...yet as we learn later, Zelda actually wants to investigate the disappearing Spirit Tracks and is upset that Chancellor Cole won't let her. Not to mention, the disappearance of the kingdom's railway system is clearly a pretty big deal, and even if people didn't believe the whole bit about the 'sealed demon beneath the ground', it should be clear to them that the tracks have some magic to them. (Explain to me otherwise how they would be able to DISAPPEAR.) Since this is all true, couldn't Zelda just demand that a bunch of guards escort her to the Tower of Spirits in light of this national emergency?
    • You could also argue that Hyrule could've had a parliament in the form of Cole as well.

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    Paying for cargo 

  • Here's the one thing that annoys me in Spirit Tracks: if all those people want me to get ice, cuckoos, fish, wood or whatever to them, why it's ME that has to pay for the cargo?! What kind of business plan is that, where the freight pays for the transport instead of the client?
    • You get pretty force gems as reward. You know, the ones that are made out of actual Life-Force. If that's not one payment, I don't know what it is!
    • Yes, but the problem starts when you reach the place where you have to buy the produce and you have no money to pay for it. Also, the force gems are not currency, but some sort of unintended consequence of the person's gratitude. Oh, and gratitude isn't currency, either.
    • I prefer to think of Link's non-profit transport business as a very elaborate community service/PR project. Not only does it repair the Hyrulian infrastructure, but the goodwill ensures a number of actual paying jobs after the whole Malladus business is taken care of. Besides, it's not like Link has to worry about fuel or repair material costs for a magical train.
    • Again, the problem is: that produce costs. If they at least bothered to give me the money to buy those cuckoos/ice/fish/wood...
    • Actually, this game is full of Money Sink Mechanics. Maybe it's because Hyrule is still in the process of being built, but everybody and their mothers charge you money for breathing.
    • They'd probably charge you for all the freight that you tend to lose due to sun damage, collisions, and enemy attacks if they gave you enough for the full "pallet" that you buy. You'd think that even if you can't convince people of Malladus's return that they'd at least recognize that you're the only engineer crazy enough to operate with the tracks disappearing and cut you some slack, but nope.
    • It should be noted that once you've completed the force gem related quests, every subsequent delivery of cargo is paid for based on what you deliver, and does turn a profit if you do a good job. Also, the first force gem you find was generated as part of a story quest, and was explained to Link then. Every subsequent delivery Link bought without being payed for was likely a string of deliberate goodwill gestures on his part intended to repair and reboot the tracks as much as possible.
    • Some NPCs actually treat Force Gems as tangible rewards for Link's service to them, going so far as to say "This is for you" or "Here, I want you to have this." And it's possible the vendors of different cargo are actually offering Link discounts off their regular prices in exchange for his help.

    Anjean fighting 

  • How did Anjean fight Byrne, if she's riding a wheel-chair? Did she expect the spirits to ascend and miraculously make her young and athletic again?!
    • The lady may look old and frail, but she's got enough magic to keep the seal on Malladus functioning and teleport both Link and Zelda effortlessly. She's far from weak.
    • Upon giving it some thought, the best I can come up with is something akin to Yoda's fight in Episode II: She uses magic to temporarily levitate and reinforce her body.
    • Take a look at Byrne as he's preparing to fight her - he's the one who dismissed his duel with Alfonzo as hardly a fair fight, yet when Anjean turns to face him, he just readies his gauntlet without any reservations. That obviously means she's capable of something, and given her expression of hope that things will be different this time, it can be presumed that Byrne knows that from experience. In fact, given how much he describes his opponents as 'only human', I'd wager the Lokomo tribe as a whole may be better, more capable fighters than some of their appearances would let on.
    • Also, it's possible that Anjean is only using her wheelchair to play up her "frail old mystic" schtick.

    One passenger 

  • If we have an actual passenger car for the train, why are we only allowed to carry one person at a time?
    • Because those passengers are total nitpicks, who'd probably just start a fight with every other passenger that comes along.
    • They all seem to be in agreement of Link's absolute dedication to the train signals, though.
    • More likely, they didn't want to program a way to keep track of how many passengers you were currently holding, where each one was going, how happy each of them was, and so on. It's probably for the best, too - as a player, having to keep track of multiple passengers would make the escort missions even more annoying than they already are. From an in-universe perspective, Link's primary duty isn't running a passenger line, and he doesn't have a set schedule or a map of where he's coming and going. He just offers people rides as they request them - if someone needs a lift to Whittleton or Papuchia Village, for example, they probably don't want to sit and wait for Link to drop some other passenger off at Goron Village or, worse, the Ocean Temple. Probably better to just sit comfortably at home and wait for when he's available.

    Interim ruler 

  • Who ran Hyrule when the only three people known to do anything administrative went AWOL?
    • The same guys who ran it in the Child-age of Ocarina of Time after Ganondorf burned the castle down. Really, this is Hyrule, land of incompetent guards and pocket-civilizations, where the ruling monarch is either called King or Princess you expect its administration to make sense?
    • It's not like there was much of anything going wrong that anyone at the castle would know about, since it seems that whenever an issue comes up, it's immediately solved by a certain, green-clad, mysteriously anonymous train engineer.

    Installing phantoms 

  • Exactly who thought that installing Phantoms was a good idea? Given that WW Link was the only person in New Hyrule to ever deal with them and how much they did to him, I sincerely doubt that he would readily recommend them.
    • Weren't they there before any of the descendants of the people from old Hyrule came?
    • It's heavily implied that the "power" that helped the spirits finally sealing Malladus was Tetra's Light-Force, since it seems to be the key to break the seal. Also, Light Arrows being the thing that defeated him. The only people known to ever use Light Arrows are Link and, especially, Princess Zelda. So I guess, Malladus defeat and the creation of the tower and the tracks occured roughly a week or so after the pirates first arrived on the continent. It was probably populated by the remaining hires of Hyrule a few months later, given that everybody states that the tracks and the tower have seamingly been there forever. Ah, anyway, to get down to the point: Anjean states that the Phantoms of the tower were originally animated by good spirits, rather than evil ones. Link probably thought "Hey, if the good guys are controlling them and not a life-force sucking monstrosity: Sure, why not?"
    • They're on his side for a change, he can vouch for their strength, and he probably had the locomo sword in his day too, so they had a contingency if they did live up to his nightmares. And it's only him who ever saw them. Tetra would take his word, but he'd be hard pressed to explain it to everyone else, given they're notably different.
    • Here's an idea - assuming the Spirits of Good are on the same level in the Hylian pantheon as the Ocean King, that is, they didn't create their respective realms, but they what they can to watch over them...Then perhaps after the events of Phantom Hourglass, the Ocean King brought up the Phantoms he'd encountered to the other members of the pantheon and how, if used for good, potentially efficient they could be. Thus, the spirits, after constructed the tower, could have expressed interest in this idea and so chose to implement Phantoms as a security system.

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    New train tracks 

  • Why didn't anybody consider building some new, non-magical train tracks to replace the disappearing ones? The problem did seem to have been going on for a good while before the game started.
    • That would be a rather large job requiring coordination between Mayscore and the Gorons for wood and iron which can't be transported because the tracks have disappeared...
      • Also, the Gorons can't even get their iron, since the eruptions near their home are keeping them from mining it.
    • It's probably also because no one knows how to build new tracks. The ones in place currently are magical deviations that the spirits themselves installed, at a time when humans clearly weren't as civilized. It's something like The City of Ember, in that regard, where everything's been around so long that no one even knows how it really works or how to fix it or make more.
    • Developers’ notes and concept art also reveal to us that the trains used in New Hyrule don’t have an external power source — rather, they run using energy they get from the Spirit Tracks, sort of like a subway system. If anyone wanted to get a new rail system put together, they wouldn’t just have to build new tracks but also find something else to use for fuel and then figure out how to incorporate it into the trains they have, or else build new ones.

    Train complaints 

  • Does New Hyrule have the pickiest train passengers in history or do they simply not recognize that it's sort of difficult to follow all traffic signals while under tank attack? Where's Link's respect?
    • It gets even worse when you realize that Link is the only engineer brave enough to still use the tracks and therefore could charge his passengers a ton of money if he wanted to. They should be grateful about the fact that they are getting rides FOR FREE.
    • By that logic, Teacher has the right to bitch at you, at the very least. He pays you 300 rupees per trip, and takes like six of them over the course of the game.
    • This so hard. I wish there was some sort of button one could press to turn Link around and have him shove the Engineer's Certificate in his passengers' faces. "Hey, do you have one of these? No? THEN SHUT THE HELL UP AND LET ME DRIVE."
    • Oh geez, I wish that button was in.'
    • All humor aside, you're free to stop the train while you're dealing with enemy attacks, so you don't have to risk missing any of the railway signals. If the passengers complained about you stopping the train too, then this complaint would be a bit more palpable.

    Cole respected 

  • How was Chancellor Cole able to fool all of Hyrule of his intentions for years?
    • The same way Ganondorf and Aginham did. Hyrulean politicians have suffered from thousands of years of not being able to notice that sort of thing, why start now?
    • Hyrule isn't the only country to suffer from Evil Chancellor-itis.
    • True, but you have to wonder why Cole didn't use any magic to conceal the giant demon horns of doom, instead opting for the suspicious gravity-defying top hats.
    • Because he's eccentric! and doesn't understand human fashion, like wizards and muggles.
    • In addition to what's already been said, keep in mind that when Link first encounters Cole, he's about 95% finished with the phase of his plan that involves posing as a human. For all we know, he could have been much better at being discreet about his plans up to the point where it didn't matter anymore. Also, if you think about it, Cole very well may have wanted Zelda to realize that something wasn't right about him, so that she would try to take matters into her own hands and leave the castle, making it much easier for him to capture her body.

    Trading Post broken bridge 

  • Why does the Spirit Track leading past the Trading Post require you to get the bridge fixed, while all the other ones that go over water provide their own support? (And if it's just because there was loose wood covering the track, why would you need a professional bridgebuilder to move it out of the way?)
    • Because the bridge is badly damaged and doesn't seem to be a part of the "normal" Spirit Tracks. If you don't want to see how well your magic train floats, you'll need a repairman who knows what he's doing on the task.
    • Keep in mind that most tracks that extend over the water (save for those within the Ocean Realm, which I presume would be designed for that) that you see in-game are the result of Force Gems you gain from transporting passengers...aren't they? Since they may not have been there before the tracks started disappearing, obviously there wouldn't be a need for people to build bridges for other means of travel alongside them, whereas the broken bridge appeared to be the previously only way of moving between the Forest and Ocean Realms.
    • Take another look at that bridge when it's broken. The parts actually holding up the tracks are completely intact. Its the wooden additions — which appear to be there so that people can walk alongside the tracks — which are broken. It's only impassable because the wooden parts fell onto the tracks and are blocking the train, the tracks themselves are perfectly fine.

    Spiders 

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    Ghost photo 

  • At the very end of the game, how did Zelda get a photograph of herself in ghost-form flying alongside Link's train? I mean, only Link could see her in ghost-form, so I highly doubt a photograph would get around that.

    Invisible passengers 

  • When Anjean and Byrne are in your passenger car, shouldn't they be visible when they transport people around? By proxy, does that mean that Link can't take anymore passengers but gets to for our sake? Do they entertain the passengers? And what would Teacher's reaction be seeing the "Sage" of the Tower out and about?
    • Uncomfortable train car moment. I wondered this too, especially since I can't bring myself to slog through the last of the Spirit Tower, and I spend all my time aimlessly wandering around the overworld. Presumably they're sitting in there as I thunder down the target range for the 5th time that day and sit in front of the snow realm blizzard maze watching that one armoured train pace back and forth for hours on end.
    • We've seen how some of the citizens of New Hyrule behave - very close-minded and ignorant in regards to things outside their own realms. Even assuming Anjean doesn't do something to render herself and Byrne invisible to other passengers, all they would probably see if they glanced a few seats down is an old woman in a steam-powered wheelchair and some sleepyhead with a ponytail and a weird metal arm. At most, Byrne might raise a few eyebrows if someone were able to tell he'd been injured, but it doesn't seem like they'd be too out of the ordinary in terms of what you'd see on a train ride through a place like New Hyrule.

    Firing the cannon 

  • Who fires the cannon? Link's busy up working the engine so it can't be him.
    • There's probably a button or something up there where Link is that can aim and fire the cannon. That or Zelda did it.

    Whip and birds 

  • The hookshot whip target bars on those birds. Who put them there? Why? And how come the birds don't get freaked out by a ten year-old flinging a whip with a snake head at their throats?
    • The Papuchians probably use the birds to get around their village, maybe. They don't freak out because they're used to it.

    Unguarded train 

  • A relatively minor one, I admit, but still...notice when you're in a town, Link's train is just sitting on the tracks, left unguarded. There is only one set of tracks; no cut-off for other trains to pass. Especially noticeable is Hyrule Castle, which can have a Phantom Train pass by. So, what? Whenever the Spirit Train isn't moving, Phantom Trains don't move either?
    • They just want to kill Link, but are restricted to the tracks. They can't kill Link when he's in town so they don't even bother. They don't care about destroying the train, they just want Link to die in a crash. That's how I interpret it. Or Gameplay and Story Segregation.
    • That just give me the funny mental image of Link walking back to the station after purchasing something in Castle Town, only to find that a Phantom Train hit his while he was away, and all that's left is a big pile of burning wood and twisted metal.
    • Remember, the original train is presumably destroyed when the tracks just disappear. When the Phantom Trains start appearing, Link is already riding a magical train. Maybe it becomes intangible whenever the engineer leaves it.
    • I like to think that the Phantom trains "turn off" and become dormant when Link is not on the rails. They only activate when Link is present on the Spirit Tracks.
    • Or each station (or at least the important ones) is more complex than it appears in-game, with sections of track apart from the main one that arriving trains can turn in to and stop at, which are safe from the monster trains.

    Dark Ore 

  • The Dark Ore. Melts in sunlight, okay, sure. So why don't they just put a tarp over it?
    • Because a wizard burned the tarp.
    • Or perhaps it melts due to some form of radiation that comes from being in sunlight...Radiation can go through a tarp, can't it? If so, the Gorons probably wouldn't know what radiation is or have a way to prevent it, so they just say, "It melts in sunlight, so move quickly."

    Tetra stained-glass 

  • Why is the stained-glass window of Tetra depicting her in her young age? Why aren't there any pieces of art depicting her as an adult? It just doesn't make sense to me. For that matter, how come no one seems to acknowledge Link's status as the Hero of freaking Winds? You know, that guy that saved the entire Great Sea from Ganon's rule? There's not even a statue of the guy anywhere to be seen. That's just disrespectful if you ask me...
    • It could also be that Link, modest as always, strongly opposed their building anything so grand as a statue to him, so they had to find a more discreet way to thank him. So they decided that to honor the guy who'd defended their princess in times of peril, the guard's uniform would look like his clothes, essentially giving the impression Hyrule Castle was guarded by an entire army of Links.
    • Don't you know? Tetra's actually 35! Seriously though, it could just be that it is her grown up, but she's Older Than She Looks. It may also be that the time of her arrival in New Hyrule, when she was young, was a momentous occasion, thus the glass depicts her young.
    • While he did save Tetra in the previous two games, there's no indication that the Hero of Winds had any special involvement in the founding of New Hyrule, beyond being just another member of her pirate crew. We don't even know if he lived long enough to see it, seeing as Anjean never mentions meeting him. His past deeds could easily warrant the guards dressing in green in his honor, but wouldn't necessitate a giant statue being erected to commemorate him.

    Other trains 

  • The first time you go out in your train, there's three other trains riding about which you have to avoid hitting, which suggests that there's at least three other engineers around. And then once you reach Castle Town... that's it. The trains vanish for the rest of the game, and everyone acts as if Link is the only person who can even use trains anymore (except Alfonzo, but he doesn't go out much). So what happened to the other three trains and their engineers?
    • It's explained by Ferrus that most people are too afraid to go out travelling with the tracks disappearing and monsters mucking about. None of the passenger trains we're shown appear to have cannons, after all.

    Age of the country 

  • Just how old is this land? The flute was given to Zelda by her grandmother, and just about every character is maybe two generations away from Phantom Hourglass. And yet in less than a hundred years people manage to forget the whole Sealed Evil in a Can thing?
    • You forget, these are largely populated by people with minds similar to those that forgot that Hyrule existed in less than a hundred years (as WW is only one hundred years after OOT).
    • The "hundred years" thing was apparently a mistranslation; it seems that they actually meant to say hundreds of years. Also, the whole backstory with Malladus is implied to take place long before Tetra's people set foot in New Hyrule.
    • Its canonical-ness is up for debate, but the Hyrule Encyclopedia provides some details that help clear up the confusion. According to it, the only inhabitants of the land at the time the spirits departed after sealing Malladus were the Lokomo, who are described as consisting of many people rather than the six sages and Byrne seen in-game. The New Hyruleans don't know anything about the sealing of the Demon King because they weren't there when it happened, due to arriving later — the most they have to go on is what the Lokomo might have told them.

    Zelda spinning train 

  • Usually when you are in the Spirit Tower you tell Anjean which way you want to go, and she'll spin the train around to face the proper direction. Okay, that makes sense. Then Anjean becomes occupied elsewhere, and suddenly Zelda can spin the train around. Um, how? Unless occupying a Phantom's body, Zelda is utterly intangible and unable to even cast a spell.
    • She's seen Anjean do it multiple times. Maybe she learned from it.
    • Also, she does cast a spell. During the Final Battle.
    • My theory is that neither Zelda nor Anjean operates the turntable, but rather the spirits, or their energy that remains in the tower, is responsible. Obviously Anjean, being their servant, would be capable of communicating with or controlling this latent power, and Zelda can as well due to the fact that she's a spirit herself and hosts some of the very same power in her blood.

    Sacred power 

  • If the sacred power of Zelda's bloodline would render Malladus unstoppable, why does he choose to attack with a laser that does a mere 0.5 hearts of damage?
    • Because the laser's main target is Zelda, in her Phantom armor - as you may notice, the laser seems to render her unable to move at the speed she would be able to otherwise. So Malladus does what he can to slow Zelda down, while Cole sends his ghost rats after her so he can use her as a puppet to attack Link.
    • And because Link's that awesome.
    • you also have to consider that Malladus JUST got revived, and is most likelly not used to his new body, or to being alive in general, think of it like if someone just woke up from an extremely long coma, and just like that they start walking around and shooting lasors.
    • Zelda's sacred power is kind of irrelevant to this discussion, by the way. The issue wasn't that it made Malladus unstoppable in a "He's so powerful now!" sort of way. All her sacred power ensured was that the spirits wouldn't be able to seal him away again once he adapted to the vessel.

    Rail Map 

  • Exactly how is it that Link obtaining a Rail Map causes the lost Spirit Tracks to reappear? And if it were that simple, why were the four of them hidden inside the Tower of Spirits, instead of just having Anjean hold on to them? Did the spirits really think it was a good idea to keep their only fail-safes against something going wrong enshrined within one of their most potentially catastrophic targets?
    • Because Anjean is (possibly) restricted to her steam-powered wheelchair and can't reach them herself, and they might have hidden the Rail Maps because the Rail Maps also include paths to where the most dangerous monsters reside. If a normal person obtained the Rail Map and opened the paths to the temples then people would probably try to enter the temples and end up getting killed by something like Stagnox or Cragma, if they even manage to make it past all of the deadly traps and other monsters.
    • Well, the boss monsters weren't installed inside the temples until Cole's plot started rolling around, and this still fails to explain why the spirits who built the tower didn't give the Rail Map to Anjean instead of splitting it up and hiding the pieces in separate rooms.

    Seeing ghost 

  • Is there any logical reasoning as to why Link and no one else can see Zelda's spirit?
    • We're supposed to assume it's because they have some sort of fated connection, or something similar. You know, with Link being the fated hero who's gonna go on this adventure with her and save New Hyrule. Not the most logical explanation, but it's at least something.
    • Apparently, according to Hyrule Historia, in the backstory to The Legend of Zelda: Skyward Sword there is implied to be an ancient, spiritual connection between the spirit of the Hero (the original Hero of Hylia) and the line of Zelda (who is Hylia reborn as a human). So this may have something to do with it.
    • Except that "spirit of the Hero" no longer existed in the Adult branch of the timeline; at the end of Ocarina of Time, Zelda sent Link back to his childhood, banishing him from her branch and leaving him (and his spirit) nonexistent and unable to return. The spirit that Zelda in Spirit Tracks is interacting with has, at most, only been around since The Wind Waker.
    • The Hyrule Encyclopedia provides an alternative explanation; the book implies that the Lokomo were once a much more far-reaching and established tribe than the seven of them we see in the game. It could be that Link has some Lokomo ancestry in him, and that's why he's able to see Zelda's spirit like they can.

    Safe zones 

  • What's the point of safe zones in the Tower of Spirits if Phantoms are normally able to enter them and the tower is owned and operated by the Spirits of Good? Who would have need of them, then?
    • Perhaps the safe zones are areas still protected by the spirits, like the safe zones of the Ocean Temple in Phantom Hourglass. So the spirits can allow 'good' phantoms to pass and block 'evil' ones.
    • I imagine that the safe zones repel demonic influence. Since the Phantoms are all controlled by Malladus' dark magic now, they cannot enter. Like with the Temple of the Ocean King before it, these zones are probably the Tower's natural state. Unfortunately, Malladus' minions cut off the power supply to the Tower which allowed evil to corrupt it to the point where only small pockets of divine protection remain.
    • I think that it was a fail safe put in by those that created the Tower. They knew that Malladus was powerful; maybe he could return and want to take revenge? They couldn't predict the future, so they chose to play it safe and install pockets of divinity.

    Knowledge of Anjean 

  • Seriously, how could no one in New Hyrule know who Anjean is? The Tower of Spirits is the centerpiece of the land, and with the turntable in the lobby, it's undeniably the most convenient way of moving between realms quickly. Is it just that somehow no one has ever gone inside it?
    • You have to remember that the tracks leading into the Tower of Spirits are magical, as well as the path to the Tower being inaccessable to the player when they lack a magical train, so normal people probably don't see/can't use the Tower's tracks, as well as the Tower being in a highly secluded area that would probably take hours on foot to reach with little gain from going there.
    • I don't recall there being anything stopping you from reaching the tower using your regular train, save for the fact that you're in a hurry to attend your graduation ceremony - Link, Alfonzo, and Zelda seemed perfectly content with going there later on, and if I remember correctly, the gate to the Forest Realm was still open. Also, the tracks leading the tower being magical is kind of a moot point. They're Spirit Tracks, responsible for keeping a demon sealed beneath the ground. They're all magical. And even if the turntable in the lobby couldn't be used at first, with the Spirit Train being encased in stone in the center, then this still begs the question why the spirits would have a turntable constructed in the first place.

    Lokomo Sword 
  • There is really no reason for Anjean not to give Link the Lokomo Sword at the very beginning of the game.
    • You could probably Wild Mass Guess it as the sword not having power until all the rail maps are complete. Or something.
    • She's pretty old. Maybe she just forgot she had it with her.
    • She didn't think Link was meant to use it. Like she said: "Until now, only the spirits have wielded this blade."
    • Also, she knows he's eventually going to have to face off against the Demon King Malladus. He'll need all the sacred power he can get. There was no reason or need to give it to him earlier - it was just Phantoms in the Tower of Spirits, and Link had the tears of light to deal with them.

    Castle Town shortcut 
  • How did Link and Zelda get back to Castle Town after the battle with Malladus? The Spirit Train makes an appearance in the credits, so we know it was around, but there weren't any tracks in the area and who knows where the actual train was at that point, since the last time we saw it was in the Dark Realm. We can't even tell where in Hyrule they were— the scenery looks like a cross between the Fire Realm and the sand portion of the Ocean Realm; the Tower of Spirits is visible, but you can see it from pretty much anywhere, so that really doesn't help. Anybody have any ideas?
    • Personally, I figured that they might just have walked... The credits montage indicates that quite some time has passed, as Teacher is back in Castle Town, no matter where you left him last. It is also possible that all of the Dark Trains vanished along with the Dark Realm's entrance, and curious people started their trains back up - Zelda and Link could merely hitch a ride back to town from there.
    • It's possible Anjean fixed the train before she departed for the heavens - it'd make more sense than her stranding Link and Zelda there, and she and Byrne were last seen on the train in the Dark Realm before they show up during the final confrontation, meaning if they had found a way to get there, chances are they brought the Spirit Train with them. Given the appearance of the surrounding mountains and the proximity of the area to the Tower of Spirits, I'd say Link and Zelda were probably left somewhere in between the Forest and Snow Realms, meaning it wouldn't be too much work for them to go looking for some tracks they could use to get back to, say, Castle Town.

     Fate of the Lokomo Sword 
  • What happens to the Lokomo Sword after the Lokomo depart for the heavens? Does Link keep it, or...?
    • Since the Lokomo Sword is (presumably) inanimate and it (presumably) doesn't have a will of its own, it (presumably) stays with ST's Link until he either puts it in a safe place or gives it to his descendants.
    • Oh...I didn't mean it like, does the sword do something to get rid of itself on its own? I was just asking if maybe the spirits had it destroyed or did Link enshrine in within the tower, or something like that, since it is a legendary artifact, and Link has never really seemed to keep any of the legendary-tier swords he obtains after his adventures are over. That's all I was wondering.
    • Most likely, it'll be entombed or otherwise protected until it is needed again like the Master Sword before it. Link went through almost the entire game without it, so he clearly doesn't need to save the day from threats short of another demon king, so it's better to ensure that it will be preserved in case some future hero requires it to fight another great evil.

     Cole should zap him, too... 
  • After he zaps Zelda's spirit out of her body, Cole has no reason to leave Link or Alfonzo alive in the field. He gains no benefit from letting them live, even if he didn't know that Link was capable of seeing Zelda's spirit, and Link would be just as likely to head to the tower for help on his own even if he and Zelda couldn't communicate anyway.
    • Remember that Alfonzo had just been punched into the train by Byrne, so Cole likely thought that Alfonzo was killed by it, or at least out of commission. As for Link, as far as Cole knew, he was just an Engineer, and thus couldn't do anything, so he wouldn't be a threat.
    • Engineer or no, Link still saw what happened. He was wearing a guard recruit's uniform, and he still had Zelda's letter asking for his help. The only reason Cole got as far into his plans as he did was because the guards were too stupid to take sufficient action when their princess disappeared.

     Zelda's arrow wound 
  • Zelda doesn't seem to be injured in any way after regaining her body, even though Link shot a light arrow through its chest moments earlier.
    • Possibly because bolts of divine light don't leave physical injuries or wounds. Electrocution would be a more likely injury to have sustained - Link is electrocuted if shot with a light arrow during the final battle of The Wind Waker - but even in that case, Malladus would've bore the full brunt of it, anyway, as he was inhabiting Zelda's body at the time.

     Anjean, you couldn't have given us that a little sooner? 
  • If Anjean had the power to conjure a suit of Phantom armor at her leisure, why didn't she consider doing that earlier in the game? Just give that right to Link, have him leave it in his train's passenger car, and then Zelda could possess it and follow Link through dungeons to help Link when he needs her. It would've been a cool way of involving Zelda more in regular gameplay.
    • while that would have been extremely cool, Anjean DID mention when she was using all of her power to keep the tower mostly in place when you first reach it, she had to focus her magic on that at all times, and most likely couldn't have afforded taking her time to poof a phantom out of thin air for zelda to use until the entire tower was rebuilt.

     Princesses who do nothing 
  • So apparently, princesses just sitting around doing nothing is a family tradition. Who started that? Tetra's rebellious daughter?
    • Tetra didn't know she was a princess throughout most of The Wind Waker, and she did just wait inside Hyrule Castle for Link to come save her after she found out. Plus, all iterations of Zelda that have appeared across the series are distantly related to each other, recall it? Her family doesn't just go back to Tetra and stop there.

     They wasted a perfectly good vessel... 
  • Instead of destroying Byrne and then taking over Cole's body to fight Link and Zelda, why didn't Malladus just possess Byrne? He's bigger and physically stronger than Cole, has a huge metal Hookshot on his arm, and as a Lokomo, he would probably have some sacred power in his veins for Malladus to feed off of...Not as much as Zelda's of course, but certainly more than Cole would have.
    • Byrne was still injured from the fight against Link and Zelda, and stopping Malladus with a force field may have used up the last of his energy, so his body was too weak for Malladus to use. Had Byrne been in better condition, he probably could have kept Malladus in the force field and survived.
    • By that point, Malladus' plot had gone completely off the rails, pun intended. He was angered beyond belief that Byrne protected his only suitable vessel and promptly killed him for it. When Cole dared to order him to take her body again when it wasn't possible, Malladus had enough and just swallowed him up instead. Taking a body besides Zelda's would kill Malladus quickly anyway, but he was so angered by that point that he didn't care anymore and just grabbed the closest one to him in hopes of bringing the whole world down with him.

     Fresh wounds 
  • Anjean and Byrne can't help with the fight against Malladus because they're still injured from their battles earlier. Why not give them some potions?
    • Apart from Gameplay and Story Segregation, it's possible their wounds were too deep for the potions to heal - most of the damage Link sustains is only done to him a little at a time, meaning it's a bunch of smaller wounds that a potion to heal easily. Or the bulk of their wounds were caused by magic (we know Byrne's was, having been attacked by Malladus), which the potion might not be capable of healing, or it won't work on them because they're both members of the sacred Lokomo tribe.

     The Spirit Flute 
  • If Zelda thought that the Spirit Flute was meant to protect her, then why didn't she bring it with her to the tower on the first trip instead of asking Link to take it with him on the second? She's little more than a ghost at that point - what is there for her to need protection from that she didn't before?
    • The (allegedly) badass swordsman Alfonzo was all the protection she thought she needed, or she simply didn't realize the gravity of the situation until the tower blew up, Alfonzo and Link got curbstomped, and she got zapped by Cole. And since Cole was able to sever her spirit from her body, she was afraid Cole and Byrne could do her worse than that (notice how scared she is when confronted by Byrne in the glyph room).
    • That's all well and good, but she admits later that she didn't know the flute had any sacred powers, so why would she think it capable of protecting her even after the levity of the situation became apparent? At that point, it's just a family heirloom, nothing more. (Also, I don't believe she knew that Alfonzo happened to be Link's mentor until they got back to the station.)

     Recruit's Uniform 
  • Why would Zelda have a guard's uniform with her in her office? And if she had one all along, why not use it to disguise herself and sneak out of the castle that way?
    • She probably took the uniform from the barracks as a plan to escape the castle. If she were to escape alone, a guard in uniform ditching the castle would look suspicious, and a princess wandering in public without an escort would attract attention. The uniform probably wasn't designed for girls either, so the poor fit would give her away.

     Ceremony 
  • Shouldn't Alfonzo, as Link's mentor, have attended the ceremony with him in the beginning? Link didn't seem to have any sort of paperwork or other certification of being ready to become a full-fledged royal engineer, so it seems as though the one who taught and tested him would be an important (if not necessary) person to have around for the event. Why does he stay behind?

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