Headscratchers / Paper Mario: The Thousand-Year Door

How do the characters with no hands get dressed?

• How does Goombella get dressed in the morning if she doesn't have hands? In fact, how does she pull out her tattle log or ANYTHING without hands?
  • The same way Homestar, Homsar, Marzipan, The King Of Town, That Little Chef Guy, 1-Up, or Cheatball does! How do those guys do it? The world may never know.
    • Mild telekinesis?
    • Yeah, it's pretty much canon that they have some sort of telekinesis. In the baseball games, a Goomba is a playable character, and they're actually above-average in pitching, despite having no arms. The bat and the glove are visibly floating around beside the Goomba◊.

Luigi in the audience

• You can find Luigi in Rogueport with a new chapter of his own adventure (and a partner to prove it) every time you return with a crystal star. Then why can he sometimes be seen in the audience of your battles? Isn't he supposed to be off on his own adventure?
  • Gameplay and Story Segregation.
  • Cosplay? Or perhaps Luigi's watching in between boat trips?
  • He's in the final boss battle if I'm not mistaken.
  • Wasn't his adventure over with at that point?
  • The entire "stage & audience" aspect of the battle isn't something we're supposed to assume is happening in-universe. Otherwise, you'd have to wonder why Grubba is okay with his power-draining machine being revealed to so many audience members, why Mario's partners don't question being on the wrong side of the stage when fighting alongside Doopliss, et cetera.

Rogueport Crystal Star

• If the Crystal Star from the X-Naut Base was originally found in Rougeport, why did it go to Fahr Outpost in the final battle?
  • It (or rather, the game designers) didn't want the Bob-Ombs to feel left out, maybe?
  • They might have been going to all the nearby towns. Because Rogueport was literally right on top of where the battle was taking place, there might have been no need for a Crystal Star to stop there.
  • Perhaps the Crystal Stars, like the Magical Map (probably because of the former), "know" where you ended up getting them. The last one you got was on the moon, but since it's populated entirely by enemies, it went to the next best place: the location responsible for getting you to the moon.

Vivian's knowledge

• So if Vivian joined Mario's party during the middle of the game, why didn't she tell them that her sisters were working for a demon that wanted to take over Peach's body? Also, the Shadow Queen seemed forgetful about Vivian's presence and made no mention of Doopliss taking her place.
  • Maybe Vivian (And maybe even Marilyn) were unaware of Beldam's plan to revive the Shadow Queen. Vivian (And as said, maybe Marilyn) probably thought that they were just working to serve Grodus.
  • Although their ages aren't clear, Beldam is statedly the oldest of the Sirens. It's entirely possible that Beldam was alive when the Queen was sealed 1000 years ago, but (at least) Vivian wasn't alive then, or was too young to be able to remember. Or maybe Beldam just never told Vivian about their real plans because she thought she was too stupid and would screw it up.
    • This is actually confirmed if you have Vivian out when you reach the Palace of Shadow throne room; she states that something about the environment seems familiar to her, hinting she was old enough to have been there 1,000 years ago, but not old enough to remember why.
• Also have to question why she didn't bother telling Mario and Co. that the X-Naut base and final Crystal Star was on the moon.
  • There's no indication she knew that they were on the moon, seeing as they do all of their travel to and from there via shadow magic. And even if she had known about where the fortress was, it wouldn't have helped Mario at any point before Peach found out from TEC. You still need the cannon in Fahr Outpost to get to the moon, you need the Ultra Hammer to get to Fahr Outpost, and you need the Ultra Boots from Riverside Station to get the Ultra Hammer.
  • In addition to all that's been said, Beldam is presumably smart enough to know the odds of Vivian pulling a Mistreatment-Induced Betrayal due to being bullied so often — and indeed, she never seems shocked or appalled once it actually happens. She wouldn't have wanted to let Vivian in on anything that Vivian could share with the enemy, with that in mind.

Hooktail's letters

• How were Hooktail and Gloomtail able to write letters to each other when the latter was locked behind the Thousand-Year Door?
  • ...Dragon magic?
  • Maybe Gloomtail just blamed someone for her not writing to him on impulse without considering a more reasonable explanation.

Nitro Honey Syrup explosion

• In Chapter 6, the rat businessman on the Excess Express mentions that his stolen product, the Nitro Honey Syrup, is capable of causing an explosive disaster if it's mixed with calcium from a seashell and a bit of gold... I have two questions about this - how would whoever created the product have come to discover the results of such a random combination, and how were the Shadow Sirens also able to discover the same information, considering their plans to use it for Mario's undoing would have required them to have done so?

  • It was said by the businessrat that the syrup could even resurrect the dead. Even if that was an exaggeration, it was obviously a pretty powerful item, so the creators likely did a LOT of research into its chemical formula. Calcium and gold, despite gold being notoriously nonreactive, could theoretically create this explosion if mixed with the syrup, which the manufacturers probably knew.
  • Going off of this, since the rat businessman was travelling with the Nitro Honey Syrup, whatever the reason — sales, marketing, promotion, investment — he'd probably have the paperwork with him detailing the properties of the concoction, including any warnings about what it ought not to come in contact with. In that case, the Shadow Sirens would've realized what it could do once Doopliss stole the briefcase.

Rogueport Crystal Star on the map

• If the last Crystal Star was originally kept with the Magical Map in Rogueport, that means that, normally, the one who found the map and brought it to the Thousand-Year Door would already have that Crystal Star. So why, when Mario's hunting for all of them, does the map reveal that one last, if it was supposed to be the first one he should've gotten?
  • Because it's supposed to be a plot twist that Peach was taken to The Moon, just like how it's supposed to be a plot twist that the legendary treasure is the Shadow Queen.
  • All part of Grodus's plan, which came to fruition after Chapter 6.
  • Less meta, the map could have selected the star that was closest at the time Mario first used it. In fact, judging by the last few stars, it could have just been selecting the closest one period. Consider the locations:
    • Petalburg could easily be only kilometers from Rogueport itself.
    • The Boggly Woods also could be relatively close.
    • Glitzville can only be reached by blimp, yes, but only because of its altitude: Kammy implies that it is a day trip.
    • Twilight Town could be farther away, considering how the time of day changes significantly between there and Rogueport.
    • Keelhaul Key is several days voyage by sail, though this may not be a direct route.
    • Poshley Heights is at least two full days away from Rogueport by train, possibly as many as two and a half, depending on the times of departure and arrival and how long Mario took to lower the bridge at the abandoned station: Even at 20 km/hr, that is at least 960 km.
    • Finally, the moon is, you know, the moon, and is almost certainly farther from any location on its planet than any other location on the planet.
    • Perhaps the Crystal Stars and Map analyzed the situation and ordered the locations by partner and equipment needs, so they won't send Mario to a place where he'll need the Ultra Boots before he goes to the place that has them, or to a place that requires Koops' shell ability before he joins the party, and so on.

Noose in Rogueport

• A bit of Fridge Logic/Fridge Horror - Who would the noose in Rogueport even be used on, when a majority of the population are Waddling Head Goombas?
  • Bandits? Toads? Koopas? Craws? Piantas? ...Anthropomorphic snails? The rest of the populace might be waddling heads (Bob-Ombs, Squeeks) or things that float (Boos, Lakitus), but there's no real shortage of kinds of characters it might theoretically have been used on, though what sorts of crimes were deemed to warrant it...
  • What would they even use that noose for, anyway? Even Rogueport doesn't seem like such a nasty place that they would perform public hangings in the central square.
  • It was probably there to hang really bad criminals, the first of which was probably the witch because they used to do that in the 17th century witch trials along with incendiary executions.
  • Another possibility is that they use it as something closer to a pillory/stock. Dangling a criminal by their midsection for a while as a way to make them miserable and publicly shame them.

Shadow teleportation

• Why doesn't Vivian ever use her power to teleport through the shadows like her sisters can to help Mario and co. when applicable? She could've traveled back to Rogueport to find someone to help the crew when they were stranded on Keelhaul Key, or went to Poshley Heights and gotten the Garnet Star instantaneously instead of Mario having to take the train. (I know the last one wouldn't have mattered since it was a fake, but she could've tried.)
  • Keelhaul Key is stated in game to have very turbulent waters surrounding it, which is why you had to seek out Bobbery. And even if another ship were to get close to the island, it would also have been sunk by the Embers.
  • There's also a blue pipe, but you need the Ultra Hammer for it.

X's Abilities: A Primer

• The phrase "X's Abilities: A Primer" is stated every time a new partner joins your party (including Ms. Mowz, the only optional party member). What does it mean?
  • A primer is a type of book, usually intended to teach or introduce something. It's meant to fit with the whole books/paper theme of the game.

The train to Poshley Heights

• Why do the Shadow Sirens waste so much time trying to stop Mario from reaching Poshley Heights, with the whole bomb threat, instead of just warping into the sanctum and taking the Garnet Star while he's forced to take the train?
  • Maybe Grodus was already setting up his plan to have Mario do the dirty work of gathering the stars for him, and therefore he and the Shadow Sirens weren't seriously trying to stop Mario? That was his logic in not stopping him during the very next chapter (by leaving the last Crystal Star to Lord Crump, his "least competent underling"). I doubt he had that plan the whole game, but by the point of Mario having all but two of the stars, I see why he would start considering it.
  • If that were the case, then a) why do the Shadow Sirens take the Crystal Star from the sanctum at all, and b) why is Grodus upset that it wound up being a fake? Each Crystal Star Mario collects is his only means of knowing where the next one is, especially since he doesn't know that the X-Nauts already have the last one, and the sirens don't break into the sanctum until Mario gets there anyway, so it's not like they couldn't have waited a few extra minutes for him to grab it.
  • Why is everyone assuming the Shadow Sirens' teleportation is instant travel? Even when they disappear into the ground they have to physically move their shadow to where they want to pop up, as evinced by Vivian in battle. Especially taking into consideration the cut parts of Chapter 6 (you were supposed to fight the Sirens at the drawbridge station, and the Smorg was created by Beldam to stop you) one could reasonably assume they were travelling by some other means, if not stowing away on the Excess Express itself.
  • Your statement about them having to "move" their shadows to their next location is kind of moot, too, since you can't really do that if you're trying to travel down to Earth's surface from an underground lunar base - there's obviously some sort of teleportation involved, and even if it's not instantaneous, it would still have to be faster than a 3-day train ride. And the things that were cut are irrelevant, too, since they still lead to the question of why the sirens are wasting so much time stopping Mario instead of warping to the sanctum.
  • From Beldam's perspective, she doesn't really have to actually stop Mario at any point, as long as somebody opens the door. She just has to act like she's trying.

Rogueport's sorry state

• Why is Rogueport stuck in such a dilapidated state? The town has the ruins of an ancient, very prosperous city buried beneath it, all of which seem to be perfectly able to be explored, as well as a huge door rumored to hold a legendary treasure behind it - seems like it would be an archaeologist's dream to go digging through all of that. Yet the reason the town's filled with cutthroats, thieves, and a crime syndicate seems to be that they go to Rogueport because no one ever looks for them there, implying people aren't interested in the treasure and the ancient city.
  • I blame the mafia, but honestly most port towns with a lot of cultural mixing end up being populated with poor immigrants trying to eke their way through their overpopulated slums.
  • As for the legend, seeing how Mario didn't realize the rumors of a treasure until 1,000 years after the door was closed, it's possible that the "legendary" treasure was a local rumor that never spread outside of Rogueport.

Train tickets

• Did Mario and co. really have to go straight to Don Pianta in order to obtain tickets for the Excess Express? Yes, the tickets are supposed to be available only to the rich and famous, but Mario is a hero of the Mushroom Kingdom and is known to a lot of people, and one of his companions he's travelling with is a supposedly world-famous actress, who was apparently wealthy enough to have her own private abode built in a secluded corner of the Boggly Woods. Even if you wanted to argue that Flurrie is retired or something like that, it still begs the question of why no one ever considers it on option before advising you to ask the mafia for a favor, right?
  • I'm sure there would have been another way without Don Pianta, but because that was the first and apparently easiest opportunity they were presented with, they went with it. As for Mario being famous, that doesn't stop innkeepers and shopkeepers from charging him the same as they do everyone else, so I don't see anyone giving him a discount here.
    • Well, you could say it was an easy opportunity, but recall that this is also the guy who told him not to come back. And your active partner tells Frankly as much. It's probably a good thing the Don was in such a bad way when he came in to ask.
  • As it turns out, the train tickets are such a breeze for the don that he offers to let Mario have as many as he likes... It's just weird that Frankly's first hint of advice whenever a problem arises is "Go see if the mafia will do you a favor for this." The way he explains it to them doesn't even sound like he's aware of what the mafia is really like.
  • The mafia controls everything that goes in and everything that goes out of the town. They decide who gets to be rich and famous.

Keelhaul Key's "Accommodations"

• Why do the inn and shop on Keelhaul Key still charge coins during Chapter 5? Not only is Mario their captain, but everyone there is stranded on a deserted island. How can they possibly be charged for things they need to survive? (And even if money is commonly found just by defeating enemies, the crew consists, in total, of Mario and his partners, Four-Eyes, Pa-Patch, Flavio, and a few Toads and Bob-ombs - I can only imagine the first three of them having the skills necessary to battle the enemies on the island.)
  • I think you've hit upon it without realizing it. They've still got to make money and get paid, but they can't go running into the jungle and fight the enemies therein, so they leave it to more capable fighters such as Mario, who later come back and (at least theoretically) avail themselves of the Toads' services.

Redemption

• How was Beldam able to get off the hook without punishment at the end of the game? Super Paper Mario showed that its villains had some personality and redeemable qualities throughout the game, but Beldam is a pretty classic case of a Wicked Witch. She tricked two groups of people into opening the Thousand-Year Door and resurrecting the Shadow Queen and never displayed any regret at having done so. How is she suddenly all nice and good come the ending? Why does the game imply as though she's already been forgiven?
  • The Japanese version of the game supposedly had Mario being brainwashed to do the Shadow Queen's bidding in the event you agreed to become her servant. It's possible she had Beldam brainwashed the entire time as well.

Punio's search

• Why didn't Punio go ask Flurrie for help before going all the way to Rogueport? Even if he didn't think she could fight off the X-Nauts on her own, he could've at least asked her to help him find someone else to take them.
  • Maybe he thought the way to Flurrie's house was more dangerous for him than attempting to find help if he went towards Rogueport?
  • But he does know that Flurrie is fond of going for walks in the woods - the fact that she lost her necklace implies she did so quite recently - and he doesn't know anyone in Rogueport. He couldn't have just hid somewhere and waited for her to pass by, even if he couldn't make it to her house?
  • Well, Flurrie didn't even want to show her face to Punio when she lost her necklace wanting to stay locked up in her room. So, I highly doubt she was going to go out for walks without getting her necklace back first. And you really think that Punio could take on the entire Shadow Sirens by himself?
    • Well, here's the thing: We know all the trouble he would have actually getting her help, but apparently, based on their dialogue, even trying to ask didn't dawn on him until he got all the way to the tree, found the normal entrance blocked by a locked door, and went to the general vicinity of the "thingy" covering the secret entrance. It's only after you go to enlist her aid that the party finds out about the necklace problem. On top of that, he would likely not know he needed to engage the Shadow Sirens to get the necklace, and they apparently aren't out for handing out random thrashings, as you can find out by talking to Beldam while the poster is still "missing".
    • And we know that the Punies have been locked up long enough for Petuni's mushroom to dry up, whereas Flurrie didn't realize her necklace was gone until Mario was already in the Boggly Woods. And she didn't know that the Shadow Sirens had found the necklace, and even if she had, I doubt she would've left it up to Punio to fight them and get it back. She trusted Mario with the task because he's...well, Mario, but if it were just up to Punio, I could see her swallowing her pride and helping him without the necklace. (Or at least going and getting it back herself.)
  • Punio's dialogue strongly implies that he's been to Flurrie's house before, as well. This has to be a case of either him or the developers just not thinking of it, as all the evidence suggests that he could have and should have gone to her first.
  • Because, as far as Punio was aware, Flurrie wasn't a combatant.
  • As for Punio asking her to come with him to Rogueport, it’s strongly implied that he wanted to be seen as a hero by the other Punies for finding someone who could save them from the X-Nauts. Flurrie could have helped him find someone more easily, but then she would’ve gotten most of the credit. Asking her to help get back into the tree was different, because Punio had already found Mario at that point.
  • If you try to go to Flurrie's house before seeing the Great Tree, she's absent. Perhaps Punio did try to visit her originally, but she wasn't there so he went to Rogueport.

Invisible Peach

• How do Peach's clothes remain visible when she drinks the invisibility potion, despite shrinking or growing with her when she drinks a botched potion?
  • For that matter, why do her footsteps still sound like shoes when she’s completely invisible?
  • Maybe Peach wears special clothing that allows her clothes to change size whenever she changes size? I can understand the invisibility since the potion is meant to affect your body directly and not what you wear over top of it. It's not like Peach has the ability to turn invisible herself like with Francis in the next game. And maybe her feet just sound that way naturally? Or the developers had to keep that sound end to make sure we still hear her walking?
  • What's the original mechanic that characterized Super Mario Bros and remains one of the series' defining features? The mushrooms that make Mario grow. Perhaps everyone in the Mushroom Kingdom wears special clothing that contorts to their bodies no matter how much they change.

Pipes in the Sewers

• Why would an ancient city (i.e. Rogueport Sewers) have pipes leading to, among other places, a presumably recently-built city (i.e. Poshley Heights), a military outpost in the middle of nowhere (i.e. Fahr Outpost), and a deserted island (i.e. Keelhaul Key)?
  • Maybe the pipes to other towns were constructed later in Rogueport's history. (And then blocked off once the town became more befitting of its name, since people didn't want just anyone from there to be able to come and go as they pleased.)
  • The same reason there are pipes leading to random, coincidentally plot-important places in Toad Town’s sewers.
  • Anyway, at least some of the places the pipes lead to were probably still around 1,000 years ago — at least two of the heroes who originally defeated the Shadow Queen were said to have hidden their Crystal Stars inside the Great Tree and Creepy Steeple, respectively. I think the same was even true for Hooktail Castle, though I could easily be misremembering.

The Thousand Year Seal

• Why did Bedlam instruct Grodus and the X-nauts - or even need them - to gather the Crystal Stars in the first place? Later on in the game Professor Frankly realizes and reports to Mario and Co. that the Seal on the titular Thousand Year Door; the Entry gate to the Palace of Shadows where the Shadow Queen's spirit resided, was beginning to fail, and in fact was weakening rapidly. He hypothesized - rightly - that the Power in the Crystal Stars had a limit and that they could only keep the door shut for roughly a millennium, and this being the thousandth year, the seal was almost about to break. With this being the case, with the seal set to be gone within the year, and with Bedlam having already waited ten centuries to revive her mistress, why couldn't or didn't she just wait a few more months for the magic of the seal to expire on it's own? Furthermore, the Crystal Stars were dangerous, gathering them together was a bad idea on multiple levels. While they were originally created by the Queen as a means to amplify her already cosmically terrifying power to unfathomable levels, they were also the instruments of her last defeat - which cost her her physical body - and the keys to the seal that had bound her, a seal that could be reapplied with the right knowledge or else their power could be used to destroy her once and for all - which is exactly what transpired. The only answer I can think of, is that Bedlam somehow was unaware of the fact that the seal was failing or that indeed it could or would fail at all. If she thought it was permanent unless undone by the Crystal Stars then, that pretty much accounts for everything, she couldn't have expected Peach to send Mario the map, and thus get him involved in disrupting her schemes, and if she really didn't know who Peach was beyond being a pure soul, perfect to open the map chest, then she might not have even figured that Mario would be involved either way - not knowing who he is at the beginning of the game supports that - unlike Bowser and his minions who plan for Mario's inevitable incursion into their plans as a matter of course anytime they try their hands at princess-nappig.
  • It's also possible that they intended to just let the seal weaken, but then they learned that the map existed and decided they needed to get the Crystal Stars themselves before someone else found the map and started looking for them.
  • Another guess: even if the Seal on the Thousand-Year Door did give out on its own, the Crystal Stars would still be out there, and as the OP said, it's clear that their power is the only thing capable of counteracting the Shadow Queen's magic. So Beldam had a vested reason for possessing them in either event: either someone uses the Stars to break the Seal and free the Shadow Queen early, or the Seal breaks on its own, but the Crystal Stars are safely in Beldam's possession and can't be used against her mistress. Beldam was essentially hedging her bets and trying to make sure that no matter what happened, she'd have the Crystal Stars, ensuring that the Shadow Queen couldn't be beaten.

Effects of the invisibility potion

• Why is Peach's shadow visible if she isn't? She's invisible, so her shadow shouldn't be there. Plus, wouldn't the potion effects wear off after a while?
  • Her shadow being visible is just a gameplay element so that players don't lose track of her while she's invisible. We can assume it's not actually visible seeing as none of the X-Nauts question it. As for the effects wearing off, they might have done so eventually, but there was no need for Peach to be invisible any longer, and she had to get dressed again anyway. Plus, she could have guards checking her room at certain intervals, and her being invisible when they found her definitely would've raised some alarm.

Yoshi's Arrival

• When Yoshi hatches from his egg, how is he already able to talk, and how does he automatically have a diaper and shoes on him. Furthermore, he shouldn't be allowed to be a Glitz Pit fighter since he's an infant.
  • Yoshis being fully capable, cognizant, and clothed upon hatching is pretty standard for the species, isn't it? As for the second question... where did you get to read the Glitz Pit regulations to know that they don't allow newborns, especially newborns as self-sufficient as the Yoshi Kid?

No protection for Peach

• An NPC mentions that Peach was in one of Rogueport's back alleys when she was captured by the X-Nauts. She's visiting the Mushroom Kingdom's closest analog of Detroit — what made her think going anywhere near the back alleys was a good idea? And why wasn't there any security there to protect her? If Toadsworth knew where their trip would take them, why not invite Mario along from the start so that he'd be there if anything went wrong?

Where did the Shadow Queen go after her defeat?

• Where do people like The Shadow Queen go when they die?
  • They get locked up in more or less the same place Bonechill was kept in the Underwhere in Super Paper Mario.
    • Maybe her soul was destroyed? (the game did mention that only her physical form was killed)
    • Pretty much the same case with Dimentio: Total cession of existence. Like the above troper said, Shadow Queen's physical form was destroyed a long time ago and only her soul remained sealed behind the Thousand-Year Door thanks to the Crystal Stars (which was why she needed a vessel). Mario then entered the Thousand-Year Door itself and using the same Stars, defeated the soul itself thus wiping out from existence.

Rankings in the Glitz Pit

• Why are the Armored Harriers the tenth highest rated team in the Glitz Pit? They have approximately one weakness, and most of the major league has no way to take advantage of it. Why aren't they higher-ranked? Have they been annoying Grubba?
  • Maybe everyone else has a move that can damage them that they never use against anyone else. Also, Grubba may be keeping them there as a Secret Test of Character to ensure only creative fighters can advance to the upper ranks.
    • If this was the case, then they wouldn't have been demoted to the minor league after being defeated by Mario.
    • Of course they would. Mario beat them fair and square, so Grubba has to let him advance and send them back to the minors. The idea is that he would try to keep them at rank 10 through the means afforded to him as the promoter. He'd just need to give them a particularly easy fight condition next time to get them back into the major league.
  • Guys like Rawk Hawk could probably pick them up and throw them at each other. Other fighters could toss them out of the ring or simply let them launch themselves from it. They're low-ranked because their "invincible bodies" gimmick is all they have, and they aren't even smart enough to take advantage of it properly.
  • Probably they don't obey the commands they are given before the battle.

Missing the match

• Much ado is made about Mario missing the title match with Rawk Hawk, and indeed, it's revealed Rawk Hawk bribed security to have him locked up so that he wouldn't have to face him. This raises the question... What are the consequences of forfeiting the match? Wouldn't Mario be able to just try again? Maybe, at the very least, he'd go down a rank or two, but unless forfeiting bans him from the Glitz Pit entirely, sooner or later he's going to be back to challenge Rawk Hawk again. And you can only bribe security guards so many times without someone picking up on what's going on, so what was Rawk Hawk going to do going forward?
  • A few reasons. First, a fighter's momentum can play a huge part in their rise to glory. Losing the title match by forfeiting would severely impact that. Secondly, forfeiting via no-show would be a critical blow to Gonzales' popularity, which would likely result in much of his fanbase turning against him, further stopping his momentum. Third, Rawk Hawk wanted to send a message to Gonzales that those who cross him (by stealing his fans, stealing his thunder, and seemingly insulting his ability as a champion) end up with the rug pulled out from under them. Under normal circumstances, Rawk Hawk would only have needed to do this once to nullify the threat to his position. Unfortunately for him though, Gonzales is the hero Mario, so even if his plan had succeeded it probably wouldn't have spelled the end of his rival.

Why isn't there a pipe to Glitzville?

• The intended logic is presumably that it wouldn't make sense to be able to get to a floating city by pipe, but why not just have a really long pipe that connects to it from the ground? Or to a set of cannons that can launch you to Glitzville and back?
  • The Pianta syndicate would probably veto any attempt to build such a pipe, since it would make their control over the airship less influential. They might've been responsible for blocking off the pipe to Poshley Heights for the same reason.
  • Ignoring the logistical nightmare of building and maintaining a pipe to a floating city held up above the clouds via rocket thrusters (which I imagine makes it not 100% stationary), most of the pipes to other locales are in dangerous and inconvenient locations. Besides, the airship is already an efficient way to transport multiple people with minimal issue. Cannons aren't a particularly viable alternative either, as no sane person would be willing to use those as transport. As for gameplay reasons why there's no shortcuts to Glitzville, the airship is fast enough that a pipe/cannon wouldn't really save any time.

Crystal Stars turned against their creator

• The lore behind the Crystal Stars is that they were created by the Shadow Queen. So why did they basically betray her? The climax of her battle shows they're sentient if they're able to return to previous places so the populace can cheer for Mario and end the Queen permanently. There's no indication they were responding to Mario's will or anything.
  • While there is a distinct lack of explanation about what the Crystal Stars manage to do during the finale, there's no reason to assume that they're self-aware to the point that they would display loyalty to their creator above anyone else. Even if they were, maybe they just don't like the Shadow Queen. Their last two sets of owners were Mario and his partners and the four heroes from 1,000 years ago. Maybe they spent so much time with the good guys that they came to sympathize with their goals.

No Yellow Color?

• In spite of how commonly Yoshis are colored Yellow throughout the Mario and Yoshi games, why isn't there a yellow palette swap availabe for Mini-Yoshi?

Pit of 100 Trials Exit Pipes

• The Pit was built as a prison for the Shadow Queen's enemies. If the enemies didn't kill them, Bonetail certainly would. This obviously makes the pipes on every 10th floor questionable.
  • Based on her dialogue during the final battle, the Shadow Queen seems to like to avoid killing people if they prove they can be useful to her. The pit could be her way of ferreting out potentially useful servants. “Ahh, I see you survived long enough to reach one of my escape pipes. Now will you join me? No? Well, back into the pit with you!”

Pit of 100 Trials Treasures

• The treasure chests and their badges (or the Strange Sack for the 50th floor). Why were they put there, and Mario's entourage couldn't have been the first people to enter, so the treasure from the earlier floors should have been taken.

Non-Undead Enemies in the Pit

• Since undead creatures don't need to eat or anything so that explains why they managed to exist in the pit, but what of the enemies that are alive, how do they survive without food, water, or fresh air? If they leave through the pipes, they're not able to enter the same way since its one direction, which would make it a pain to get back to the floor they're stationed.
  • They're probably just physical manifestations conjured by the Shadow Queen.

Warping to the Moon

• How are the Shadow Sirens able to warp from anywhere on Rogueport to the Moon? It is often shown they sink into the ground to travel, but there is no ground in space.
  • Same way Mario can return: the teleport room in that abandoned house in buried Rogueport.
  • If the above were the case, you’d think Vivian would have told Mario about it. They aren’t going into the ground to teleport; they’re sinking into the shadows, which happen to be on the ground. There’s nothing saying their magic relies on two places being physically connected.

Tricking the Partners

• How was Doopliss (as Mario) able to convince the party members to go back with him to his home? They already obtained the red Crystal Star from him, so there was no need to return. And wouldn't they find it strange that "Mario" has a different voice and talks in full sentences?
  • The partners all seem to know that they’re back at the steeple to fight Shadow Mario and Vivian. And they don’t mind following you all across the world anyway, but Doopliss probably told them something like “Hey, I just noticed! That shadow creep used his powers to swap our Crystal Stars for the one we got from beating him! Let’s go beat him again and take them all back!” That’s not too far off from what really happened, and would be of enough importance for the partners to go along with it.
  • As for Mario speaking in full sentences, all four of the partners comment on this if you speak to them in the mayor’s house. They all note that it’s out of character for him, but choose to just go with it with varying degrees of reluctance.

Palace of Shadow's condition

• For a place that's over a thousand years old and has been underground for that much time, the Palace of Shadow is in surprisingly exceptional condition and is completely intact compared to the rest of the ancient city underground. How did it manage to stay in that condition even after the calamity that left much of the city in ruins?
  • Seeing as the Shadow Queen was responsible for the calamity that befell the ancient city, she wouldn’t have wanted it to affect the palace considering it was her own stronghold. Besides, some of the ruination that befell the ancient city could have happened after its initial downfall, in the form of looting, scavengers, natural disasters, etc. that wouldn’t have affected the palace because the door was sealed.

Star-themed stuff in the Palace of Shadow

• If the Palace was built by the Queen underground (assuming it was) then what is the point of there being the Planetarium and decor and things themed after stars if it never saw the sky? The same thing would be asked about the stained-glass windows, too, as these kinds of windows typically are for being illuminated by outdoor sunlight.
  • It wasn’t underground originally. The palace is just a portion of the ancient city that the Shadow Queen took over, and the city didn’t sink underground until some point during her reign. As for the planetarium, it’s mentioned that the queen was interested in utilizing celestial power, since she created the Crystal Stars for that purpose. That’s one reason why she would’ve invested in a planetarium.
  • Another possibility is that the planetarium was a part of the city before it was taken over. The architecture of the courtyard outside the tower resembles that of the ruins in the Rogueport sewers rather than the rest of the palace, and if memory serves, the partners comment on how different the atmosphere is there.

No recognition

• Glitzville is presumably in the skies of the Mushroom Kingdom, yet pretty much nobody there recognizes Mario or Bowser!
  • Rogueport and the areas connected to it seem to take place in an area separate from the mainland of the Mushroom Kingdom; not everyone recognizes Mario. Jury's still out on Bowser. At the same time, only Grubba himself was stated not to know Bowser in Glitzville, calling him a nutcase who tried to ambush Mario.
  • Although, a select few characters such as Goombella and Koopie Koo do recognize Mario, so it could be possible Bowser garnered a bigger reputation due to his appearance and evil deeds (because really, who's going to care about an overweight middle-aged man dressed like a plumber compared to an intimidating fire-breathing turtle with access to weaponry and an army?).

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