Summary
Paper Mario: The Thousand-Year Doorhas a frankly bizarre universe with even stranger characters inhabiting it. Of course, a lot of what happens can be brushed aside for the sake of plot convenience or the sheer silliness of it, but that doesn’t mean it makes sense. If anything, as you progress throughout your adventure, you may find yourself with questions that you absolutely cannot get answers to.
That doesn’t mean that your questions are silly or should be ignored; they can just give way to interesting discussions and theories. There will probably never be a definitive answer, but these questions should be asked nonetheless.

8So… Are The Toads Wearing Hats?
An Old And Still Unresolved Debate
Sure, this technically isn’t a problem in Paper Mario, but it is an answer players have been seeking for a while. As you play through the game, you may notice that a majority of the Toadettes seem to have hair coming out from underneath what could be considered their toadstool cap.
One could easily assume that this means that the “caps” actually are just that - caps. Cultural headwear that all Toads wear. However, when you’re in Glitzville, if you talk to some characters in the Juice Bar, they imply the opposite, commenting on the pink spots on Toadette’s head. Which, in turn, puts everyone right back to square one with the debate.

7What Would The X-Nauts Do After Conquering The World?
What Would Their Perfect World Have Looked Like?
Power can be an excellent motivator for someone to do, frankly, horrible things or wield horrible intentions. However, power is not a motivator within itself - in effective storytelling, the quest for power and control only functions as a means to an end.
So, just why does Sir Grodus want to rule the world?He certainly talks a lot when on-screen, proclaiming how he loathes Mario(oddly specific) and yet keeps it very vague when it comes to his exact plans.

What has made him a compelling enough option that he has garnered a seemingly unending collection of minions and absolutely awful commanders and generals? At the end of the game, the X-Nauts pretty much gave up on their goals, so they either changed viewpoints really fast or were just shown that the plan for “perfection” really wasn’t that good in the first place.
6Why Did The X-Nauts Really Keep Princess Peach?
She’s A Liability And Not An Asset
Aside from Sir Grodus basically calling Princess Peach his pet, there really wasn’t any reason to keep her after they realized she just… didn’t know anything. In fact, when Peach confronted him about in disguise (thanks to TEC’s help), he still talked around the subject and basically told her, “Because I said so.”
Realistically, Princess Peach remaining in the base was far more of a liability than any sort of benefit - had they released her and sent her on her way, Mario would have taken much longer to reach the Moon. This, likely, would have given the X-Nauts and Sir Grodus far more time to prepare and lay out the perfect plan.

5What Did Bowser Plan To Do With The Crystal Stars?
Nobody Else Can Have Them, Apparently
Bowser very obviously did not set off with the intent to hunt down all of the Crystal Stars so he could free the Shadow Queen. More than likely, he didn’t even know what the Shadow Queen was or where she was, and instead, he just happened to see something that everyone else wanted.
Of course, if everyone else wants that thing, then he needs to have it because he’s the most evil and, therefore, should have it. In many ways,this makes Bowser an incredibly fun and relatively relatable character(who doesn’t understand that jealousy of wanting purely to keep from being excluded?).

The same logic could be applied to his obsession with Princess Peach, really. Of course, that begs the question of what Bowser planned to do once he got his hands on the Crystal Stars. Was he just going to put them on display and marvel like they were hard-won trophies?
4Why Does Doopliss Join The Shadow Sirens?
Perhaps Desperate Times Call For Desperate Measures
Although, with the power of the Ruby Crystal Star, he could make anyone into a Shadow, Doopliss is likely not a Shadow himself. Perhaps with Vivian jumping decks to go and join Mario, Beldam and Marilyn were desperate to fix up their crew again. Perhaps Doopliss was just that desperate to try and get revenge on Mario.
Whatever the case, a clear answer is never really given for their alliance, much less why Doopliss stuck around after seemingly becoming Beldam’s new punching bag. Maybe it was a combination of a lot of reasons, fueled by a desire for revenge on all sides and the knowledge that working in a group is more likely to be successful.

3Why Did Vivian Forgive Her Sisters?
Forgiveness Should Be Earned
Going through the endings, it really does seem like Vivian was the one to re-initiate with her sisters, forgiving them for being cruel to her without prompt from them. Perhaps this notion speaks to the fact that Vivian is a kind soul who dearly loves her sisters, regardless of how awful they were to her.
However, it wasn’t necessarily like Vivian was on her own. She had new friends and, more than likely, a new place to live if she so desired it. Her sweet nature (and great abilities)made her a delight to have around as a partner and as a friend.

This forgiveness almost seems less like a genuine, wholesome moment and more akin to Nintendo desperately trying to argue that family should always stick together and forgive one another. Beldam and Marilyn were not owed Vivian’s kindness or her forgiveness, and yet she offered it anyway. Did they take the chance to apologize first? Did they ever actually care for Vivian in the first place?
2How Did TEC Manage To Survive?
Nobody Is Allowed To Die Here
After Sir Grodus discovered the plot to free Princess Peach that TEC had been working up, the computer’s consciousness was subsequently destroyed - or so it seemed. Yet, this is a Paper Mario game, and death really isn’t in the cards for any of the characters you meet.
This means that when TEC is revealed to be alive, waiting for when it can meet Princess Peach again, you may be left a little bit baffled. How did it happen? Why did TEC decide to come back? Did it have a backup copy of its own consciousness somewhere? A copy that remembered Peach so fondly it could only wait for her to return?

It’s never clearly explained, and you’re really only left to make your own theories. One thing is for certain, though - TEC must be horribly lonely now.
1Why Do The Black Chests Think They’re Handing Out Curses?
They’re Really Conveniently Timed Gifts, Actually
Why do the Black Chests seem convinced that what they’re doing is actually a curse? If anything, they’re just providing awfully convenient curses that are easily controlled. Perhaps they’re just playing a little prank and having fun with it? Maybe they’re actually convinced what they’re doing is evil and wrong?
That last theory is a bit hard to believe, given that the final Black Chest actually apologizes and asks if everything is all right, though. Or, maybe, due to their isolation, they’ve forgotten how normal beings in the Mario Universe usually act and react and have spent a bit too much time reveling in ideas of chaos and revenge when really, at their core, they’re actually nice and helpful.