Paper Mario: The Thousand Year Door is the 2004 GameCube sequel to the original Paper Mario and the second game in the Paper Mario series. It starts like a lot of Mario games, with a letter from Princess Peach. She wants Mario to meet her at a distant town called Rogueport, to help her search for a legendary treasure indicated by the map she sent along with the letter. By the time Mario actually pulls into port, Peach is gone, and for once it's not Bowser who kidnapped her (and he's very, very peeved about that).The mysterious Secret Society of X-Nauts and their leader, Sir Grodus, are the ones responsible this time. They're after the same treasure as Mario, and are hanging onto Peach for an unknown purpose related to this treasure hunt. Mario learns from the Goomba Professor Frankly and his young assistant Goombella that said treasure is locked behind the eponymous Thousand-Year Door beneath town, and that opening the massive door involves collecting the Crystal Stars scattered across the surrounding regions. As the game goes on, the nature of the treasure and why the X-Nauts are holding Peach comes to light, and let's just say said treasure is not a pile of gold coins.The game retains the same paper aesthetic, Turn-Based Combat, Action Commands, and Better than a Bare Bulb humor of the previous game, with some extra tweaks introduced. Action Commands are also needed for the Limit Break moves that are attained with each Crystal Star. The previous game's damage-reducing button presses during enemy attacks are supplemented by a Blocking Stops All Damage mechanic with a narrower window of accuracy. Each battle is fought in front of an audience that must be pleased by a good performance in order to increase the amount of Star Power recovered per turn. Your partners now have a health meter, and can be incapacitated if they run out (though the battle will still go on as long as Mario is alive). World exploration is aided by Mario gaining several paper-themed transformations like a paper airplane and a paper boat.Lastly, this is the game that introduced the Cerebus Syndrome that the Paper Mario sub-series became famous for. Not only is the Evil Plan of the X-Nauts surprisingly dark for a Super Mario Bros. game, but the individual Chapters often have their own self-contained sinister elements. While later Mario games such as Mario & Luigi: Partners in Time and Luigi's Mansion: Dark Moon would also explore the Mario-verse from a more menacing angle, The Thousand-Year Door was the very first to delve into darker material than what is typical for the franchise.
Absurdly High Level Cap: Level 99. Good luck trying to get Mario up to that number because every time you level up, the star point value of every enemy goes down by one, and you will eventually reach a point where every battle only gives you one star point.
Absurdly Spacious Sewer: Rogueport Sewers, but in truth it used to be the prospering town narrated in the opening of the game.
Accidental Misnaming: Mario is referred to by various NPCs as Murphy, Marty-o, Gonzales, and Luigi, among other names.
Action Commands: Every attack has one or more of these. Pulling off certain hidden commands will even refill your star power meter.
Adaptation Decay: The in-universeSuper Luigi books, which novelize Luigi's (mis)adventures in the Waffle Kingdom. Among other things, they claim he played "a purifying earth spirit" in the Jazzafrazz Town play, when he was actually an inanimate patch of grass on the side of the road (but the town was full of Dayzees who idolized nature, and thus he was hailed by them). In fact, everything portrayed in his books except for the ending are absolute lies, starting with the very first paragraph in the series. Just listen to his partners. They'll tell the truth.
And I Must Scream: You know those black chest spirits that curse you?Those are the four heroes that sealed away the Shadow Queen, but she laid a curse on them beforehand to trap them.
And the Adventure Continues: Both in Gameplay and Story: Gameplay wise, you do stuff in Rogueport after the final battle. Story wise, it ends with Peach coming to Mario's house and saying she's found a new treasure map in the castle and is waiting for Mario on the boat. The look on Mario's face and the music just fit at that moment of the utter surprise/despair of having to go on another adventure so soon.
And Your Reward Is Clothes: There are two badges you can collect to change Mario's outfit. One is the L Emblem, found in the Poshley Sanctum, which makes Mario's outfit have Luigi's color scheme. The other can be bought from Charlieton, the W Emblem, which gives Mario Wario's color scheme. Wear them at the same time, and you get Waluigi's color scheme.
Anti-Grinding: Eventually, you'll only get 1 star point from battles, so it's best to move on with the plot rather than stick around and fight.
Ant War: The Punis aren't exactly insects, but their war with the "rival tribe" of mosquito like Jabbies plays out as this trope.
Backtracking: Pretty egregious considering every chapter except the last one involve doubling back at some point. Chapter 4 is the worst in this regard because you have to travel from one end of the map to the other and back 3 times.
Beef Gate: Gus, though he can be bribed as opposed to beaten up. You, with good timing, can have him be the very first enemy you beat in the game with perfect countering, meaning you won't take damage. It should be noted bribing only works until you come back, beating him up puts him out of the way for the rest of the game.
Berserk Button: Implying (intentionally or unintentionally) that Rawk Hawk is weak is a bad move, as he'll either go to great lengths, even cheat, to prevent the accuser from commenting on it as a means of exacting revenge on the accuser, or directly attack the accuser (although the latter did not end so well for him as the person who accused him, Bowser, was more than entitled and justified for saying that).
Big Bad: Sir Grodus, until it's revealed that he was Beldam's pawn he whole time.
"Blind Idiot" Translation: An isolated instance: Sky-Blue Spinies that have curled up into balls are referred to by the game as "Sky-Blue Pipes". Paipo is the Japanese name for Spiny Eggs, which may be where the confusion came from.
Blocking Stops All Damage: You can Super Guard against pretty much anything that causes damage in battle, regardless of whether that means physical attacks, projectiles, lightning strikes, falling walls, fire or explosions. All with no harm done to Mario.
Bonus Dungeon: The Pit of 100 Trials, though it's a good idea to go to at least floor 50 for any playthrough, as a bigger item bag is always useful.
Book Ends: It ends how it started, with Peach wanting to treasure hunt again.
Boss Bonanza: The Palace of Shadow contains boss fights against Gloomtail, the Shadow Sirens (and Doopliss), Grodus, Bowser and Kammy together, and The Shadow Queen. Arguably also the two battles with the Dark Bones, too, as they have HP on par with early-game bosses and are among the enemies whose Tattle entries can show up in Professor Frankly's wastebasket.
Boss Remix: Lord Crump, Sir Grodus, and Bowser all get this treatment.
"You out there in front of the TV!" If Goombella is your partner when Professor Frankly says this, she'll lampshade it with "Why do we always have to break through the fourth wall?"
When asked to describe Stewart in Glitzville, Goombella will mention that Cheep-Cheeps have been around since the first Mario game, and then say "I just broke through the fourth wall there, didn't I?". If you get her to describe the gatekeeper in Twilight Town, she'll mention that the game would be too easy without him, before flustering and saying 'What? I didn't say anything!'
If you defeat Gus in Rogueport, he will exclaim, "You video-game heroes ALWAYS do this!"
After Bowser goes through Rawk Hawk's secret training facility, Rawk Hawk will point at the camera and presumably ask the player if they forgot about him.
An NPC in Petalburg mentions wanting a game called "Paper Luigi". Later, he says that he's playing a new game... called Paper Mario: The Thousand Year Door. Oh, and he also finishes it before you do. He also mentions Fire Emblem, another game by Intelligent Systems. And at the end of the game? He's playing Super Paper Mario!
When you are in the Keelhaul Key chapter, at one point, the pirate "Four-Eyes" (a.k.a. Lord Crump) looks at the TV and tells the audience not to tell Mario who he obviously is. Weirdly, if your partner is Goombella at this point she will have just broken the fourth wall in Chapter Four and then acts confused when someone else breaks the fourth wall in Chapter Five.
When Koops is reunited with his father after the first dungeon, he says "Everyone thought your game was over!" This may have been an example at the time, but it no longer remains so. With the release of Super Paper Mario, the common term for death in-universe has become Game Over.
Breather Episode: Chapter 3 is the only chapter to have absolutely no connection with the main plot whatsoever.
After catching the Yoshi egg in Glitzville, Mario is given an option to, instead of free him, say "Let there be hot dogs!" Of course, picking this option will simply result in Mario's partner yelling at him and overriding his decision.
Immediately afterward, Mario is given an option to bring the egg with him or not. If he says no, his partner immediately changes his mind.
The player must open the chest in Creepy Steeple to proceed any further.
Chekhov's Gunman: When you first visited the Rogueport Sewers, you notice a small creature who runs away in a hole whenever you approach him. He becomes prominent in Chapter 2 when he's revealed to be Punio, a Puni who was trying to seek help as the X-Nauts captured his home. He follows you around for that chapture.
Chick Magnet: Every female party member kisses Mario when they join ... must be the 'stache. Even BELDAM thinks he's handsome. What can we say? Chicks dig the 'stache.
Also the mysterious lady in the Glitzville juice stand, who is very heavily hinted to be Jolene. Near the end of the game this is confirmed but at that point the woman is actually Prince Mush in disguise.
All of the Koopas, with the possible exceptions of Koops and Koopie Koo. Mario also runs into a few Shiver City penguins, all of whom are just as spacy and excitable as they were in the last game, you betcha!
Colour-Coded for Your Convenience: The Shadow Sirens' hats are indicative of their elemental powers. Vivian's is red (fire), Beldam's is blue (ice), and Marilyn's is yellow (lightning).
Colour Coded Stones: The crystal stars which must be collected throughout this game are coloured as such. The diamond, emerald, ruby, sapphire and garnet stars are white, green, red, blue and reddish-orange, respectively. Another star is palette swapped for gold and referred to as the "gold star", despite it being obvious that the star is a crystal not a metal. Perhaps a slight inversion as the last star is an iridescent white, yet it is the "crystal star" not diamond.
Continuity Nod: At the beginning of the game, Parakarry from the first Paper Mario game delivers a letter to the Mario Bros. In the post-game, you can meet another of your party members from Paper Mario 64. There would've been more than just the two, but they were Dummied Out. Jr. Troopa can also be seen in the background of a picture attached to e-mail sent to Mario by Zip Toad. Also, in Hooktail's castle, the note written by a dead Koopa is addressed to his son Kolorado, an NPC in the first game.
Crippling Overspecialization: Somewhat literally played with the Hammerman and Jumpman badges- each grants 1 extra damage for either Hammer or Jump attacks in exchange for being incapable of using the other.
Crosshair Aware: Magnus Von Grapple 2.0 sucks up audience members and uses a crosshair to aim them at Mario. It's just for show, though.
Cursed with Awesome: The black chests curse you... with the paper abilities you'll need to explore the next area/dungeon. One of the few instances where this is played for laughs. It's also justified by the fact that the "demons" are former heroes who are exploiting a loophole.
Cute Bruiser: The nameable, color-customizable Yoshi partner found in Glitzville.
Peach, but like in the first game, she does a little more than just sit around and wait to be rescued. at the end of the chapters, you get to play as Peach sneaking around the X-Naut Fortress, looking for information to help Mario.
Luigi gets his own in the form of Princess Eclair.
Darker and Edgier: The Thousand Year Door is definitely darker and edgier than its predecessor. Let's start with the opening shot of the prologue looking right at a gallows in the middle of town. The aptly named Rogueport is a textbook example of a Wretched Hive, predominantly inhabited by cutthroats and miscreants. Many of the areas in the game - notably Twilight Town and its surrounding areas, Riverside Station, the Pit of 100 Trials, and the final dungeon itself - have a creepy atmosphere by any standard, let alone those of the famously family-friendly Mario franchise. There is a dark undertone that permeates throughout the entire game, and as the plot begins to unfold, players come to the realization that the ultimate motive of the X-Nauts is far more sinister than anyone could have initially imagined, with potentially world ending repercussions.
Dark Is Not Evil: There's Twilight Town, and even your own party member, Vivian.
Mario has to sign a contract that Grubba gives Mario to participate in the ring while advising him not to read all of it, and in fact, sign without reading it. Some of the lines in the contract include Mario not being able to leave the Glitz Pit until Grubba releases him. Oddly enough, Mario can leave Glitzville via blimp after signing the contract without any repercussions.
Death of a Thousand Cuts: The Yoshi partner specializes in doing lots of damage in 1-point increments, though he can't hurt enemies with Defense. Any sort of attack boost will cause the little guy to do ridiculous amounts of damage, though.
Did You Just Punch Out Cthulhu?: Mario defeats the demonic Final Boss by jumping on it and hitting it with a hammer. ...After being powered up by the Crystal Stars, admittedly.
Difficult but Awesome: The Super Guard requires better timing than the standard guard, but nullifies all damage and deals damage to some attackers.
Disappeared Dad: Koops' father, Koopley, left for Hooktail Castle ten years before the start of the game to slay Hooktail. It doesn't end well, which gives Koops the motivation to join Mario to avenge his dad. When they defeat Hooktail, though, the dragon spits up Koopley, who survived in his stomach for ten years.
You could count Kolorado's father. Since he suffered the same fate Koops thought of his father.
Disproportionate Retribution: Rawk Hawk goes to great lengths to prevent Mario from fighting him or from advancing. Why? Simply out of revenge for Mario and his partners allegedly calling his champion's belt fake and thus inadvertently implying that he was a bad fighter (and they weren't even talking about the belt itself, but the crystal star on him). Similarly, the Armored Adonis Twins in the same chapter wanted to beat Mario to a complete pulp, and later attempted to ambush Mario right after Mario defeated another group after losing to them in a rematch because Mario allegedly talked trash about their mom (something he didn't even do, but Grubba did while pinning the blame on Mario).
Downer Ending: This pretty much happens if you decide to become the Shadow Queen's servant, as the game says "The Shadow Queen engulfs the world with her foul magic. For Mario, Peach and the world it was... GAME OVER .
The Dragon: Lord Crump. Beldam also counts, though she is The Dragon to the Shadow Queen and is actually the Big Bad of the game due to her manipulation of Grodus.
Elite Mooks: Koopatrols (which have their own elite version, Dark Koopatrols), Elite X-Nauts, Elite Wizzerds, Red Bones, Dark Bones.
Elopement: One subplot involves the daughter of a Pianta mafia don eloping with one of his underlings. The first time you meet, he agrees to secure you a ride to the place where the next Plot Coupon is if you bring them back. On finding them, they return of their own accord and he tells them to get lost but gives them his blessing in a roundabout way. They settle on a tropical island a few chapters later. In the next chapter you need a ride once again, so you return and find him sick (literally) with worry about them. One subquest later and you have your ticket, the couple and the Don reconcile and everyone's happy.
In the "Super Luigi" book series, Minister Crepe, who called for help, turns out to have been behind the kidnapping all along.
Jolene is an inversion: Although it seems like she was the one who was making the fighters disappear, it was actually her boss, Grubba, who did the deed. And while she was trying to betray him, it was actually due to the fact that she wanted to stop him knowing how much of a scumbag he really was.
Played With in Twilight Town with the crows. Mario and Vivian learn by eavesdropping on the crows how to learn the name of the monster who stole his body. Of course, they have to listen to the right crows, or they get nothing but random philosophy.
In Chapter 3, while in the vent, the person you're spying on basically goes over his entire diabolical plan to himself. Just to grab your attention, he more or less says "And since I'm talking out loud here, I'll just put this extremely important piece of paper in this desk drawer here and leave. Ah, there we go. Right there in the drawer, nobody's gonna steal it at all."
Cortez has many similarities to Johnathan Jones from Super Mario RPG. Both are pirates, both have the fifth star (which happens to be blue in both cases), and both of them become your allies and help you defeat a boss who wants to steal it from the heroes.
Merlon, Merluvlee, and Co. Explained in game, by Mr. Wonky (an NPC whom you pay for information), that they're from a tribe that names people according to profession, hence why this trend continues into Super Paper Mario.
False Innocence Trick: Although it appears that the beings trapped in the black chests were originally the four heroes of legend and thus good guys, the end result is the same nonetheless. They plead for Mario to let them out, so of course, he does. They curse him as thanks. Kind of subverted, because the curses help you, to the point that you literally cannot continue without "acquiring" them.
Food Porn: Classic Paper Mario food cooking in all its glory. You'd be surprised how good cartoony 2D food can look.
Foregone Conclusion: Luigi's Adventure. Before Luigi actually finishes his adventure, the book based on his adventure starts to release. The first volume of Super Luigi's first paragraph starts something like this: Have you ever tried your hardest to do something, fail, and then feel like you completely wasted your time. This is a story much like that. Now, this is a pretty accurate statement, consideringthe source. Except for the fact that Luigi isn't done with his quest yet. He won't be for at least two more chapters of Mario's Adventure. How does the book know?
For the Evulz: Doopliss, who curses the people of Twilight Town to transform into pigs as an ironic prank.
The Fourth Wall Will Not Protect You: Because the game's battles take place on a stage, various monsters will attack the audience, eating them, stealing their souls, using them as machine gun ammo... It interestingly also works in reverse, audience members will throw rocks and items at those in battle, they'll run on stage and give one side some power or mess something up... Not to mention their cheers refill the Star Power meter (you can get more by using stylish moves), or that you can cause some of them to explode and take out those sitting next to them.
Rogueport, as it contains many pirates as well. It even has a gallows.
Get On With It Already: The cursed chests. By the fourth cursed chest, even Mario, mute as he is in these games, is getting tired of the whole rigmarole. The cursed chest ends up quite hurt by the whole thing.
There is a noose prominently displayed in the middle of Rogueport. The way it is displayed means that the hangings are public, similar to old towns back in the day.
This game seems to delight in getting gang and drug references past the censors.
One is the gang war between what are essentially the wealthy Mafia (The Yakuza in Japan) and a poor street gang.
There are also conspicuous skulls jammed on stakes on either side of Rogueport. Note that this is a common way for a drug dealer to mark his territory.
One of the troubles deals with bringing a mysterious package to someone in the back alley of Rogueport.
At one point before Chapter 3 Professor Frankly says the Phrase "Assuming will just make" before cutting himself off and instead just ends it saying "well you know the saying" meaning he's referring to the old phrase "Assuming will make an ass out of you and me". Flurrie's response makes it even more obvious. "Oh, yes. How inappropriate."
Princess Peach winds up being naked on more than one occasion, as well, although the player can never see her (either she's showering or she's invisible).
A relatively minor example, but when tattling Fuzzies, Goombella will remark, "these things really suck...HP."
Everything that has to do with Flurrie, from her appearance to the fact that her breasts make noise when they gainax. She is the source of subliminal boob jokes. Where does Mario grab when she uses her blowing ability?
Just what the hell IS Smorg? note A scene cut from the game showed that it was something sent by the Shadow Sirens. You were supposed to fight the Shadow Sirens in the basement of the train station, but this was all cut, so it's never explained where Smorg came from in the final version. Also, there's an NPC that pops up randomly on the Excess Express post-Chapter 6, a Goomba researcher, who heavily implies that there's more of them, wondering what the feeding habits of the wild Smorg are, then asking you if you've seen one, which you must have by then.
Luigi parodies this; after beating the Chestnut King, what he could only describe as a huge nightmarish monster appeared that he took out. The Super Luigi books say it's Minister Crepe, but it's unsure which is the true story.
Heads I Win, Tails You Lose: Subtle, but you can only continue by having your body-switched fake Mario defeat the real Mario. Makes sense at the time, when the player doesn't realize they've been switched.
Here We Go Again: The end has Peach finding another treasure map and inviting Mario to come with her to search for the treasure.
Hero of Another Story: Luigi goes on his own adventure to save a princess, and even writes books about it!
Heroic Mime: Mario, almost. He speaks, but only as dialogue responses chosen by the player. Goombella lampshades this during Chapter 4 after Doopliss has switched places with Mario. "Wow... You, like, NEVER talk!"
In-Game Novel: The Super Luigi books, a novelization of Luigi's tales from that game.
Intellectual Animal: The crows in Twilight Town discuss such things as renewable energy sources and Internet start-up companies.
Interface Spoiler: Each time you finally get your hands on a Crystal Star, the game will tell you about its special powers in battle and what they do. So when you get the Ruby Star in Chapter 4 only to move on without learning about its abilities, you know something's up.
Kaizo Trap: This is possible, but you have to be very unlucky. Occasionally, at the end of a battle, the final attack will cause the stage background to fall after the enemies are dead, but before the victory dance. In the off chance that you have only 1HP and forget to defend (which is likely, as this is the nature of a Kaizo Trap), you will die.
Karma Houdini: Beldam and the Shadow Sirens. Despite loyally serving and unleashing an unspeakable horror upon the earth, they get off with a few apologies and promises. Doopliss even goes on to be an actor with Flurrie. It becomes averted for Beldam and Marilyn, who get defeated by Mario (and possibly Vivian) and justified for Vivian (Chapter 5) and Doopliss (End Of Game) as they both did a Heel Face Turn.
Mass Monster Slaughter Sidequest: One of the troubles you can take on at the Trouble Center is "Roust These Cads!", in which you are expected to fight all the enemies in the Boggly Woods for a reward of 20 coins (plus drops and Star Points).
Magic Map: One of the main objects is actually called the Magical Map. It's mostly blank at first, but each Crystal Star Mario claims causes the map to get filled in with the location of another. Said Crystal Stars tend to fall into various characters' hands and move about before Mario starts tracking them down, and despite it being made a thousand years ago, displays locations as they are in the present, such as a suburban neighborhood or a Space Base.
The Man Behind the Man: Beldam is this, as Grodus appeared to be the Big Bad right up until he succeeded at summoning the Shadow Queen, only to get zapped into nothing but a head, and it was revealed that he'd been manipulated all along.
The Bowser interlude after Chapter 6 happens to take place riiiight in front of that huge chest in Rogueport that has been taunting you the whole game, but you might have forgotten about by now. This clues the player into the fact that you can finally get it now.
The one time you catch the Pianta Syndicate doing anything really bad is in the prologue, when Tony and Vinny ambush and mug a passing pair of Robbo Gang members (Gus and Garf?), which lets you know that Rogueport isn't just rough around the edges, but actually dangerous.
Beldam is a pun on "beldame", an old-fashioned English word for an ugly old woman. It's also a play on "bedlam" with the two middle letters swapped around.
TEC's full name is TEC-XX. Since 'X' is pronounced as "cross" (as with the X-Nauts), the two Xs could be said as "double cross", appropriate given the character's role in the story.
Middle Child Syndrome: Marilyn of the Shadow Sirens. Although being the strongest, she doesn't have too big of a role compared to Beldam and Vivian. However, Vivian is usually the one that's abused/left out.
When Mario ('Great Gonzales' to everyone at this point) walks into the arena of the Glitz Pit before his fight with Rawk Hawk, the camera makes a short pan over the entire crowd, who is unanimously shouting "Gonzales, Gonzales!" except for one person who quickly shouts "Jumpman! Wait... what?"
You can also buy from Charlieton a badge named "Jumpman" which prevents you from using your Hammer but raises your Jump power by 1.
A Hammer Bro in the Glitz Pit mentions his grandfather (who he inherited his hammer from) being from World 7-1.
Never My Fault: Never Beldam's fault, shifting blame to Vivian, and later to Doopliss. Marilyn rarely gets blamed for anything, but she's not exactly respected, either.
Nice Job Breaking It, Hero: Happens when Mario and co. are tricked by Doopliss (disguised as Professor Frankly) into opening the Thousand-Year Door so the villains can get through. However, it's implied that this was for the best in the end anyway.
Nice Job Fixing It, Villain: Near the very end of the game, the only reason that Grodus doesn't manage to kill Mario is because of a timely, accidental interruption by Bowser.
No Fair Cheating: By altering the Gamecube console's internal clock ahead for joining Rogueport's daily lottery multiple times, the event will be blocked until you talk to Lucky the Bob-omb to apologize by buying another lottery ticket for 500 coins.
No Fourth Wall: The reason why you have to go all the way to Creepy Steeple, get the letter "P", and go all the way back is because Doopliss stole it. Yes, he stole the letter "P" from the keyboard.
No Hero Discount: No matter what town you save, they'll still charge you money for everything. Even the recovery blocks require coins, the amount of which is marked on top.
Nonstandard Game Over: Three: the first is if you fail to escape the Spike Room in Hooktail Castle in time, the second is if you read the diary a Toad ghost explicitly told you not to read during the Excess Express level, and the third is triggered if you agree to the Deal with the Devil before the final boss fight.
Not Rare Over There: After returning to a mafia Don who was part of a previous quest, you find him deathly ill and his bodyguards promise you the tickets for a trip on the Excess Express you need if you find his daughter and son-in-law (who he exiled at the end of said quest). On recovering when they return to his side he's furious...until you state what you were promised; he bursts into laughter and asks how many you want.
NPC Roadblock: Zess T. keeps you out of the west side of Rogueport after you break her contact lens. She doesn't budge until you buy her a new one.
In a rare case of one being able to harm you, near the climax of chapter 2, a time bomb is set off in the Great Boggly Tree. When you reach the base of the tree, the Puni elder confronts Lord Crump, resulting in her spending some time complaining about her back.
I love you. I love you. I love you. I love you. I love you. One hundred times and they actually count them out! And only one per text box. Thank Nintendo for the B button.
Overused Running Gag: WHEE HEE! FOOOOOLS! It's made clear that Mario has gotten tired of this by the fourth chest. "Spare me the prologue and just curse me already."
Pass the Popcorn: All fights have an audience watching. No matter what situation they're in. And being in the audience can be hazardous during boss fights: Hooktail the dragon takes a bite out of the audience to restore HP, after which the battle spills into the stands; Cortez does the same, but with the souls of some of the viewers; Lord Crump fires audience members at you from a cannon, and the Shadow Queen subsumes the entire audience to heal herself fully, putting you in a very sticky situation.
Peninsula of Power Leveling: You can encounter Amayzee Dayzees in the fourth chapter. After gaining the fourth chapter's Star Power, you can go to the area where they're found (preferably under the effects of the special spell that can sometimes double your experience), use said power to quickly defeat them, and bask in the levels.
Portal Network: The Mario franchise's signature pipes are required to get to most areas.
Post Final Boss: Unusual, smaller-scale example. Cortez is the "final boss" local to Chapter 5, and the end-of-chapter bells and whistles occur after his defeat, but then you have to have a miniboss battle against Lord Crump before everything is at peace for the chapter.
Mario has a "Mailbox SP", which looks exactly like a Game Boy Advance SP.
There's a kid NPC in Petalburg who goes on about an awesome new video game he's playing. The title? Fire Emblem.
The monitor you use to reserve a fight in the Glitz Pit in TTYD is a Gameboy Advance.
Pennington also "deduces" that what the young Bob-omb Bub wants for his birthday is a Gameboy Advance "because that's what all the kids want these days".
Prophecies Rhyme All the Time: "Hold the Magical Map aloft before the entrance to the Thousand-Year Door. Then the stars will light the way that leads to the stones of yesterday."
Punch Clock Villain: Most of the lesser X-Nauts. Implied for most of the game with their over-casual nature and general uncoordination in the area of Mookery, and confirmed if you examine the chem lab notes with Mario: "I have some stuff to do, so I'm not coming in to work tomorrow, and that's that." Also, they tend to appear as audience members.
Punny Name: Most of the Toads have one, like the cook, Zess T., or the heavy eater, Heff T.
Luigi's team is even better. He's got a crispy floating squid, a living bomb that looks like a cherry, a disgruntled mechanic who builds roving death vehicles, a spacey actor, and a mysterious thing that must deliver a package. All of them are with Luigi to keep him from doing/not doing something or other.
"Rashomon"-Style: In most cases, the story Luigi tells contrasts with the account given by the partner. Interestingly, only the very first account is irreconciliably contradicted by that of Luigi's partner (Blooey in this case)—and it's also impossible to take Blooey's account as complete truth, as it fails to explain how Luigi secured that second compass piece. Mostly, the partners' conversations are used to reveal their real motivations for following Luigi around.
Recognition Failure: This is a Running Gag; whenever Mario meets a village elder, they're behind the times and don't recognize him (to the annoyance of their younger relatives).
Retirony: In chapter 3, KP Pete announces his plans to retire from the Glitz Pit after his match with Mario. After the match, and his retirement, he ends up stumbling on Grubba's use of the Gold Star, the real one to maintain his youth, and ends up silenced. A slight twist in that he doesn't end up killed, although he is certainly beaten to a huge pulp and barely even able to breathe.
Go ahead, ignore the repeated warnings and read that diary... you'll get a Non-Standard Game Over for your troubles.
In Chapter 3, there is a cake delivered to the locker room just after you accept the 2nd seed battle. Fall for it by eating it, and you won't have your partner for the next battle. Don't, and Shellshocker, the Shady Koopa, will be on the floor, unable to move. Subverted with a similar cake delivered earlier in the chapter; that one will actually recharge your HP, FP, andStar Power.
Schrödinger's Gun: Right after Zess T. tells you about her lost contact lens, no matter where you move, you will always end up stepping on them.
Screw This, I'm Outta Here!: About halfway through the game, Vivian decides that she's fed up with Beldam's abuse and leaves to join the mysterious shadowy person, even sticking around once he's revealed to be Mario.
Sequential Boss: Cortez, and later Grodus, followed immediately by Bowser and Kammy.
Shape Shifter Guilt Trip: Not quite an exact use, but referenced: When the Shadow Queen takes over Peach's body at the end, Goombella tells you that no matter how much it looks like your friend, you can't think of it that way and just have to fight it.
She's a Man in Japan: Vivian is a transwoman in the Japanese version, but this was removed in the English release. The other European localisations stick to the original Japanese script and consider her either a transvestite or transgender.
Likewise, Bonetail is referred to as female in some translations of the game.
Shoo Out the Clowns: After Lord Crump's defeat, the story starts to become nightmarish and disturbing.
The Toad who fought the Shadow Queen with a Goomba, a Boo and a Koopa could be this to the Japanese fairy tale of Momotaro, who fought off a demon and its entourage with the help of a dog, a bird and a monkey.
Sunglasses at Night: The Dark Koopas (this is actually lampshaded by Goombella when she wonders why they wear sunglasses in the depths of a cave).
Surprise Creepy: In particular, the final boss is a pretty jarring development in a Mario-branded game.
Suspiciously Similar Substitute: Several of Mario's party members in this game are functionally identical to the ones in the first game. This is most obvious with party members that are the same species, such as Goombario and Goombella, or Kooper and Koops.
The Dev Team Thinks of Everything : Even if you do know Doopliss' name, you still have to spell it just like that for him to accept it. Trying to replace the missing lowercase p with an uppercase P will not work. That's an obvious, yet clever way to prevent players from cheating and skipping a lot of that chapter.
Theme Naming: The dragons Hooktail, Gloomtail, and Bonetail.
Unexplained Recovery: TEC caused the X-Nauts' base to self-destruct, but after the game is completed, not only is TEC still alive and well, bue even the damn base is intact. Not even he has a clue how it is possible.
The Un Reveal: Subverted. If you save a game clear file and go back to visit Frankly, he'll reveal that the treasure was... a dried shroom, which is apparently an amazing discovery, as it reveals that people ate mushrooms one thousand years ago.
Visual Pun: One of Luigi's companions is a cherry Bob-omb.
We Cannot Go On Without You: Continued from Paper Mario 64, but made even worse due to Mario's partners now having their own HP values. If Mario's partners bite the dust, you continue as normal. If Mario goes down, it's game over, even if your partner is healthy enough to finish off the enemy party.
What the Hell, Hero?: There are several instances when Mario can choose between two things to say, and sometimes the second choice is less than morally sound to say the least. If he chooses that option, his partner will chew him out and, in a case of seeking the next course of action, insist on taking the first option. (For one example of these options, see the sub-note under Egg McGuffin.)
"Where Are They Now?" Epilogue: Goombella sends a letter to Mario at the end, detailing what happened to his partners and several other important characters.
What Happened to the Mouse?: We never do get to see what became of Bowser and Kammy at all during Gombella's travels when she tells Mario what everyone is up to. Heck, the last time they're ever seen in the game is lying in defeat in the Palace of Shadow just before the final boss fight, and they disappear after you leave the room and aren't mentioned at all during the ending. However, this being the constant Big Bad of Mario games, he's bound to return.
Xanatos Gambit: Grodus pulls one of these by leaving the final Crystal Star with Lord Crump, so that his plan would work regardless of whether Crump lost to Mario or not.
Yin-Yang Clash: The Iron Clefts' bodies can withstand any attack... and their spikes can pierce anything. You defeat them by knocking them into each other.
You Are A Tree, Charlie Brown: Luigi performs in a play and gets the role of... grass. He's the only one who never got any lines, either. Subverted, however, in that he was playing to an audience of flowers. Grass is very important to them, so they absolutely adored him!
Your Mom: Grubba basically delivers some trash talking (which he attributed to Mario) to the Armored Harriers/Iron Adonis Twins, with one of the trash talks also revealed to be a veiled Yo' Mama joke, as he mentions that outie belly buttons run in the family, causing the Iron Clefts to get very angered at Mario, as their mother has an outie.