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Paper Mario: The Thousand-Year Door is a role-playing game, being the second installment in the Paper Mario series. It was developed by Intelligent Systems for the Nintendo GameCube in 2004. It revolves around Mario, who embarks on a mission to rescue Princess Peach and save the world from the X-Nauts, particularly their leader, Sir Grodus. To do this, Mario and his partners should collect the seven magical artifacts known as the Crystal Stars in order to open the Thousand-Year Door, a mythical door which has a lot of rumors spread about.

Being a sequel to Paper Mario, the game retains the same artstyle and key elements as obtaining various party members that will help the player on solving different puzzles or getting Star Points by winning a battle. However, the game improves these elements further such as partners having Heart Points, or activating the Star Power by interacting with the Audience rather than refilling it automatically. Additionally, the game introduces paper abilities, which come across with paper-like aesthetics and act similarily to partners, allowing the player to solve the missions.

Prologue: A Rogue's Welcome
The adventure begins when Princess Peach goes on a cruise to Rogueport where she meets a hooded woman, and buys a box which contains a map. She sends this to Mario, along with a letter asking him to help her search for the map's treasure. Soon after that, she is kidnapped by Sir Grodus. Mario receives the letter with the map and decides to help her, and thus boards a ship to Rogueport.

Shortly after Mario reaches Rogueport, he finds Lord Crump attempting to interrogate Goombella about the Crystal Stars. Mario intervenes and Lord Crump tries to defeat him. After defeating the X-Naut general and escaping from the X-Nauts, Goombella introduces herself, and Mario explains his quest to her. As Goombella is also searching for the map's treasure, she decides to join Mario. Then, Goombella suggests to go to Professor Frankly's house, to consult him and show him the map. At the professor's house, Frankly explains that the map is related to the legend of the treasure of the Thousand-Year Door, and that, to obtain the treasure, one must first open the door with the seven Crystal Stars. Said objects can be found by holding the Magical Map before the Thousand-Year Door, which is located in the town's sewers. So, Mario holds the map before the Thousand-Year Door, revealing the location of the first Crystal Star.

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Chapter 1: Castle and Dragon
Mario and Goombella show the updated map to Professor Frankly, who reveals that the first Crystal Star is in Petal Meadows. To reach this place, they must find a pipe in Rogueport Sewers. After finding it, Mario and Goombella arrive in Petal Meadows, where they see Hooktail and her castle. The duo stops at a nearby village called Petalburg and discover from the mayor that the dragon Hooktail has been terrorizing the village. The mayor tells them that Hooktail guards the Crystal Star in her castle, and that to access it, they must find the two stone keys in Shhwonk Fortress. After finding them, Mario and Goombella march to Hooktail's castle, with Koops in tow (who wants to defeat Hooktail to avenge his dead father and become stronger). After navigating through the castle's traps with the help of Koops, they encounter the dragon and defeat her, allowing Koops's father to get out of the dragon's gut and present Mario with the Diamond Star.

Somewhere else, it is revealed that Princess Peach was abducted by the X-Nauts. When a X-Naut tells Sir Grodus someone got the first Crystal Star, Peach accidentally blurts out Mario's name. Grodus hears this and orders the Shadow Sirens to steal the map in Mario's possession. Peach then meets TEC-XX, who develops an interest in Peach's concept of love, and asks for her help to understand it. Peach agrees; in exchange, TEC lets her send e-mails to Mario. During another scene transition, at Bowser's Castle, Kammy Koopa tells Bowser about Mario's quest to find the Crystal Stars and Peach's abduction, things that motivate Bowser to hunt for the Crystal Stars and kidnap Peach back. Bowser and Kammy then head for Rogueport.

Back in Petalburg, the group receives an e-mail from Peach, who tells them she has been kidnapped. Mario and co. head back to the Thousand-Year Door to reveal the location of the next star.

Storyline text ''Mario and friends finally got a Crystal Star in the castle after defeating Hooktail. Koops even reunited with his long-lost father, whom he thought was dead. Yet they were unable to learn anything about the whereabouts of the princess. Where could Princess Peach be? Yes... Mario's adventure has only just begun.''

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Chapter 2: The Great Boggly Tree
The second Crystal Star is revealed to be in the Great Tree, home of small creatures known as Punies, deep inside Boggly Woods. When searching for the pipe leading to Boggly Woods in Rogueport Sewers, Mario and his partners encounter Punio, who tells them that the X-Nauts have invaded the Great Tree, capturing most of the Punies and that the Jabbies, the Punies' enemies, have allied with the X-Nauts and are trying to expulse the Punies from the Great Tree. Mario and co. decide to help out the Punies, and therefore Punio leads the group to the Boggly Woods. After getting there, Mario and co. encounter the Shadow Sirens with a necklace, who do not recognize him due to having lost a sketch of him. The group continues and arrives at the Great Tree. However, they realize that the tree is locked. Punio suggests they find Madame Flurrie; to find the secret entrance. However, upon reaching her home, Flurrie reveals she has lost her necklace and does not want anyone to see her without it. After defeating the Sirens and returning the necklace to Flurrie, she joins them in their quest. The group finds the secret entrance and enters the tree; after freeing the locked Punies with the aid of a special orb and after solving the Great Tree's puzzles and defeating the Jabbies, they reveal the second Crystal Star at the bottom of the tree. There, Lord Crump snatches it, and activates a time bomb to blow up the tree. After chasing him to the entrance, he stops the bomb and uses Magnus von Grapple to fight the heroes, but he is defeated by the group. Afterwards, the X-Nauts evacuate the tree and Mario and co. obtain the Emerald Star.

At the X-Naut headquarters, the X-Nauts inform Sir Grodus that Mario has taken the Emerald Star. Meanwhile, TEC-XX calls for the Princess, and asks her to dance with him. TEC then lets Peach e-mail Mario.

Bowser can be seen arriving in Petalburg, and then talking to what he thinks is Peach, but is revealed to be a poster by a nearby Koopa.

As Mario and his team move on, they receive another e-mail from Peach, who tells them that the X-Nauts are searching for the Crystal Stars. Mario and his team reveal the location of the next Crystal Star, and they visit Professor Frankly for details.

Storyline text ''And so, after pummeling Lord Crump, Mario obtained the second Crystal Star... With the X-Nauts gone, peace once again prevailed throughout the Great Tree. The Boggly Woods echoed with the Puni songs of joy. But... this may not be the last our hero hears from the vile X-Nauts. They will surely continue to stand in Mario's way and try to put a stop to his efforts...''

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Chapter 3: Of Glitz and Glory
The third Crystal Star appears in a large arena on a floating town. To reach Glitzville, Mario and the gang must visit Don Pianta. He offers them the ticket they need after doing him a favor. Once Mario and his team arrive in Glitzville, they enter the Glitz Pit, a popular place in which fighters brawl, and spot the Crystal Star on the Champ's Belt, held by Rawk Hawk, the current champion. They sign up in the Pit, battle through the ranks, and eventually gain a newborn Yoshi as a partner. Soon, a mysterious figure known only as "X" starts sending cryptic e-mails to Mario. The e-mails lead Mario and his partners to discover that the Star on the belt is a fake, and that the real Crystal Star is being used by Grubba, the promoter of the Glitz Pit. Mario & co. expose his wrongdoings and chase him into the arena, where he transforms into Macho Grubba in order to eliminate Mario and his friends. However, the group manages to defeat him. After the battle, Jolene, Grubba's assistant, appears and reveals herself as the mysterious X, explains her story, and gives Mario the Gold Star.

At the X-Naut base, TEC-XX asks Peach to go ask Grodus a question relating to his plans. The Princess goes undercover in an X-Naut disguise and learns that Grodus is plotting to use the Crystal Stars to take over the world. TEC allows her to send this message to Mario. Meanwhile, Bowser and Kammy are searching for one of the Crystal Stars in the Great Tree, where they discover that Mario already obtained it.

Mario & co. receive another message from Peach; they promptly reveal the fourth crystal star's location.

Storyline text ''Glitzville's seamy underside was a dark, dangerous place seething with conspiracy... With the help of the lovely Ms. Jolene, Mario revealed Grubba's true identity... And acquired the third Crystal Star by defeating the monstrous Macho Grubba. Grubba had used the power of the Crystal Star to run his power-draining machine... What other hidden powers might these strange and mystical items possess?''

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Chapter 4: For Pigs the Bell Tolls
Professor Frankly tells the group that the Crystal Star is located in Creepy Steeple, near Twilight Town. When Mario & co. get to Twilight Town, they discover that the village is under a curse cast by a monster who lives in the steeple. Using a new Black Chest Demon power, the group reaches the steeple, and battles the monster. During the battle, the monster uses an ability to steal Mario's name and body, transforming Mario into a shadowy version of himself. Mario's partners claim the Crystal Star and leave with whom they think is Mario. Meanwhile, the Shadow Sirens are in Twilight Town, planning on defeating Mario and his partners with their new weapon: the Superbombomb. However, Beldam seems to have lost it, prompting her to blame Vivian and to force her to search for it. The real Mario returns to Twilight Town, and helps Vivian with her problem. Out of gratitude, she joins Mario's party. They eventually discover from the monster's parrot that the monster's name is Doopliss. After telling Doopliss his name, he is weakened and flees to Creepy Steeple. Mario and Vivian chase him there and they fight once more. Mario and his new partner defeat Doopliss, allowing Mario to regain his name and body and obtain the Ruby Star.

At the X-Naut base, TEC-XX asks the Princess to participate in a sort of "quiz show" with him. By doing this, she discovers what the "treasure" of the Thousand-Year Door really is: the soul of an ancient demon. The Princess then relays this information to Mario. Meanwhile, Bowser continues his quest for the Crystal Stars by flying to Glitzville in his Koopa Clown Car. However, it malfunctions halfway there, and he travels underwater to return to Rogueport. After he and Kammy return, he orders Kammy to continue her research on the Crystal Stars.

Back in Twilight Town, Mario and his friends receive the message from Peach. They reveal the next Crystal Star and visit Professor Frankly for details.

The English name for the chapter, as well as its Japanese, Spanish, Italian, and French translations, are referencing the Ernest Hemingway novel, . The Japanese name is also potentially a reference to the Japan exclusive  co-developed by Intelligent Systems which involves a bell capable of transforming frogs into people.

Storyline text (fake) ''Mario defeated the scourge of Creepy Steeple and found the fourth Crystal Star. The people of Twilight Town have surely recovered from their awful curse by now. At this rate, Mario's quest to collect all seven Crystal Stars will be done in no time! With his back to Creepy Steeple, Mario sets out toward his bright future...''

(real) ''Mario defeated the rogue who had stolen his name and appearance. Now Mario has four Crystal Stars. That leaves a mere three more to find! And THAT means his quest to collect all of the Crystal Stars is more than half over! Now Mario heads off toward his next adventure with his new friend, Vivian... ...But what about Beldam and Marilyn? And what became of the doppelganger, Doopliss?''

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Chapter 5: The Key to Pirates
The fifth Crystal Star is located deep within a pirate's lair on the southern island of Keelhaul Key. To reach the island, Mario enlists the help of Flavio and Admiral Bobbery. They sail to the island with some Toads, Pa-Patch, and Lord Crump in disguise (known as "Four-Eyes"). On their way to the island, Mario and co. are attacked by Cortez's Embers, which shipwreck them on Keelhaul Key. Later on, some of the crew members are attacked by more Embers, and Bobbery sacrifices himself to save them. Bobbery says he is close to death, and after giving him his last request, they find out that he just fell asleep. After Mario wakes him, he joins Mario's party. With the aid of Bobbery and Flavio's Skull Gem, Mario and co. enter Pirate's Grotto. After solving some puzzles, and after gaining another ability from a Black Chest Demon, they finally reach the lair of Cortez. After they battle, Cortez gives Mario his Sapphire Star. Afterwards, Lord Crump abandons his disguise and tells Mario that he will continue attacking him with his ship's cannons until he hands over the Crystal Star. With the help of Cortez's ship and Flavio's Skull Gem, they defeat the invading X-Nauts, along with their leader.

In the X-Naut base, TEC-XX wishes to gain access to a disk in Grodus's room, and asks Peach to help him. After making an invisibility potion, she helps him and he promises to analyze the data. Peach then sends another e-mail to Mario, informing him of this. Meanwhile, in Twilight Town, Bowser and Kammy Koopa run into Lord Crump. The three get into an argument, which escalates to an armed confrontation between the Koopa Troop and the X-Nauts. However, Bowser inadvertently ignites the Superbombomb, knocking out both armies.

Back at Keelhaul Key, Cortez ferries Mario and his teammates to Rogueport. Mario gets the e-mail from Peach, telling them about what TEC is analyzing. Mario and his team then reveal the next Crystal Star's location, and visit Professor Frankly for information.

Storyline text ''Cortez, scourge of the seas... Mario soundly defeated this fearful spirit and claimed the Crystal Star. Perhaps the peaceful citizens of the world no longer need fear Cortez and his fell ship... The only problem remaining is how Mario will escape this isolated island... And could there be another problem still, hiding beneath our hero's nose?''

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Chapter 6: 3 Days of Excess
The sixth Crystal Star is in Poshley Sanctum in the town Poshley Heights. The only way to reach the town is on the famous Excess Express. After doing Don Pianta another favor, he gives Mario a train ticket. During the first day on the Excess Express, Mario and his team found many mysterious happenings, including thefts of items and messages threatening to blow up the train. On their second day of travel, Pennington, a Bumpty detective, helps Mario and his friends solve the crimes and they manage to capture a fake Zip Toad who was really Doopliss in disguise, and was the one who attempted to halt the train by causing an explosion with some stolen items. At sundown, when the train stops at Riverside Station for refuel, Doopliss escapes capture. Mario and company find that the drawbridge has been lifted, preventing the Excess Express from continuing its route. The gang enters Riverside Station and flips the switch to bring the drawbridge back down. They discover that a group of Smorgs are behind it. On the third and final day of the journey, a stowaway Smorg monster attacks the train, kidnapping all of its passengers. Mario and his friends defeat the creature, rescuing the passengers in the process, and finally reach Poshley Heights. They venture into Poshley Sanctum, a museum that happens to belong to Pennington. The Shadow Sirens, who happen to be already inside, snatch what appears to be the Garnet Star and flee. However, Pennington reveals that what they stole was a fake, and lets Mario find where the real Crystal Star is. After some exploring, Mario and company manage to find the real Garnet Star. Back at the X-Naut base, the X-Nauts tell Grodus that Mario has six of the seven Crystal Stars. They also tell him of TEC's betrayal. Meanwhile, TEC tells the Princess the data he gained from Grodus's data disk, and prepares to help Peach escape. Before he is able to, Grodus enters with two X-Nauts and orders them to initiate a data-wipe procedure of TEC's memory. TEC tells Peach "I love you" just before he is shut down.

Meanwhile, Bowser is searching for another Crystal Star in Rawk Hawk's workout room, which he has found in the form of the Champ's Belt. However, he quickly learns that it is not a real Crystal Star, just a glass fake.

Mario and his team return to Rogueport and receive an e-mail from Peach, telling them about what the X-Nauts plan to do with her, but an important part of it is cut off due to TEC being shut down. Back in Rogueport, Mario and co. reveal the next Crystal Star's location and visit Professor Frankly for details.

Chapter 6 appears to allude to , which also involves several peculiar passengers on a train where a crime takes place.

Storyline text ''Mario found the sixth Crystal Star, hidden craftily in the Poshley Heights sanctum. Now only one Crystal Star remains... But our hero still does not know where Princess Peach is being held. Where could the last Crystal Star be? And where is Peach being held? Hoping this Crystal Star might yield answers, Mario and friends return to Pennington.''

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Chapter 7: Mario Shoots the Moon
The last Crystal Star appears to be on the moon. To reach the moon, Mario and his companions travel to Fahr Outpost to find a cannon to shoot them to the moon. After searching for Goldbob and General White, whose blessings are needed to operate the cannon, Mario & co. enter the cannon and are shot to the moon. On the moon, the group discovers the X-Naut Fortress. Once they arrive at the end of it, Lord Crump appears, bragging about his latest creation — Magnus von Grapple 2.0, and tries once more to defeat Mario and company. After Lord Crump is defeated, the Crystal Star is released.

Meanwhile, Bowser is searching for another Crystal Star in the Poshley Sanctum. A Paragoomba flies in and tells Bowser that Mario has collected every Crystal Star and is heading for the Thousand-Year Door, which contains a great treasure. Bowser announces that he will steal this treasure and defeat Mario.

As Mario and his allies prepare to leave the fortress, they discover that all of the doors have been locked, except for one. In this room, the heroes find TEC, who is running on backup power. He recognizes Mario and tells him to rescue the Princess, who has been taken to the Palace of Shadow, a place that lies beyond the Thousand-Year Door. He then activates an emergency transporter. The group is transported to a room in Rogueport Sewers. After exiting the room, Professor Frankly meets them at the entrance and urges them to open the Thousand-Year Door.

Storyline text ''The last Crystal Star had been hidden in the X-Naut hideout on the moon... But by the time Mario recovered it, Peach had already been taken away... Where could Peach be now? And what of the elusive Grodus? Perhaps he holds the key to the remaining puzzle... Mario finally has all seven Crystal Stars... Where will they lead him next?''

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Chapter 8: The Thousand-Year Door
After Mario has received all seven Crystal Stars, the time has come to open the Thousand-Year Door and enter the Palace of Shadow to rescue Princess Peach from Grodus.

Mario and his friends open the Thousand-Year Door with the seven Crystal Stars, allowing them to enter the Palace of Shadow. The palace itself is full of enemies, puzzles, and traps. Eventually, Mario and co. battle and trounce a dragon named Gloomtail, older brother of Hooktail. After the dragon's defeat, he relinquishes the key to access the Riddle Tower. After solving the puzzles of the tower, a secret passage which leads deeper into the palace is revealed. Mario and his party continue down that path, but not before defeating the Shadow Sirens, who try to get rid of them. Finally, Mario and company reach the throne room of the palace, where they find and defeat Sir Grodus. Bowser and Kammy, who drop in unexpectedly, also battle Mario, but are thwarted in the end. Grodus uses the distraction of the battle to bring Princess Peach into the deepest part of the palace. There, he opens a sealed coffin and frees the Shadow Queen, the ancient demon of legend. Beldam suddenly appears and announces that she was the one who orchestrated the plot to free her mistress. The Shadow Queen refuses to be controlled by Grodus, and fries him with a lightning bolt, apparently killing him. The Queen then possesses Princess Peach, using her as a vessel to sustain her life. The world is then covered in darkness. Mario and his allies fight the Queen, but she eventually decides to fight in her real form, in which she is invincible. She proves too much for the group to handle, however, the Crystal Stars suddenly react to the evil of the Queen and fly throughout the world, each returning to where they were found, allowing the people of the world to cheer on Mario and his party. The hope of the people of the world break through the Queen's invulnerability, and this also allows Peach to give the heroes the last of her power. Strengthened, the heroes seal the Shadow Queen forever, saving the world.

Goombella later sends Mario a message, explaining what everyone has done: she works with Professor Frankly, while Koops plans on becoming the Mayor of Petalburg. Flurrie has returned to the stage and enacts "Paper Mario" as her comeback smash while Doopliss plays the role of Mario. The Yoshi fights in the Glitz Pit as the "Great Gonzales Jr.", while Vivian has forgiven her sisters and lives in Twilight Town. Admiral Bobbery sails the seas with Cortez, and Ms. Mowz runs her Lovely Howz of Badges. Lord Crump, Grodus and the X-Nauts survived and are spending their time in Poshley Heights. TEC survived as well, and hopes to see the Princess again one day. The game ends when the Princess visits the Mario Bros. with another treasure map.

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Gameplay
In terms of gameplay, Paper Mario: The Thousand-Year Door brings over the core mechanics of the N64 original and enhances them. Mario now has a voice used for jumping and attacking, and starts his adventure with a hammer. Action Commands can also be performed from the start. However, he has lost the ability to Spin Dash from the original game.

The partner system is also enhanced. Unlike the original, where partners had a simple fine/injured status system, this game gives partners their own Heart Points. As such, partners can fall in battle, and items such as the Mushroom can be used on them as well. Several partners are similar to ones seen in Paper Mario, like Koops being the counterpart of Kooper, but generally have more abilities available. Timed moves are more abundant in this game. In addition, battles are set up on a stage, like a play; this greatly affects battles, and characters can interact with the audience and stage.

Background
Another element introduced in Paper Mario: The Thousand-Year Door is the background scenery, which is actually accessible for Mario through certain pipes. Several places which only appear in the background can be visited this way, some of which include Hooktail Castle, the Great Tree, the X-Naut Fortress, and Merlee's house in the Rogueport Sewers. This feature was carried over to the next game in the series, Super Paper Mario. Certain abilities are disabled here, however. Mario's partners cannot be used in the background, Mario cannot move to a different screen/area, and he also cannot walk past any houses or locations.

Intermissions
After each chapter, there is an intermission where the player is able to control Princess Peach, who is held captive in the X-Naut Fortress. The Peach intermission is followed by a Bowser intermission, a new addition in Paper Mario: The Thousand-Year Door. Bowser usually visits the places Mario has been to one chapter before, and several missions include a side-scrolling platformer level in the style of Super Mario Bros.. In these levels, Bowser has the ability to breathe fire, and by using the only available item, the Meat, is able to radically increase his size, allowing him to crush everything in his way. While enemies like X-Nauts charge at Bowser, others like Goombas are actually scared by him and turn away when he approaches them. The levels are called 1-X, 2-X and 3-X in reference to the world numbering of Super Mario Bros., while X stands for the number of tries Bowser has used for the level. He has endless lives for the levels. They are set in the three basic terrains of Super Mario Bros.: Overworld, Underwater and Underground/Castle.

Paper abilities
Whilst exploring the game's world, the player encounters black treasure chests, which give Mario special abilities to use in the overworld. They all base on the paper element of the game's graphics.

Mario's partners
Throughout the game, Mario, just like the past game, uses partners. His partners have purposes in both the overworld and battle. They can be upgraded by Merlon by giving him 3 Shine Sprites. Every partner knows two moves upon joining the party, learns the third after being upgraded to Super Rank, and masters the final move after attaining Ultra Rank. Initially, each partner may only be upgraded once, but upon finding the Up Arrow in Hooktail's Castle, Merlon remembers he has an Ultra Stone, subsequently allowing the player to upgrade a partner for a second time.

Battle system
Battles take place on a stage. In addition to the traditional turn-based combat, the characters on-stage interact with the scenery: sometimes the background falls, damaging all characters on stage and possibly making them Dizzy, the audience helps Mario gain Star Power and also may throw items on stage or attack Mario and his partners, and lastly, some bosses even use the audience to their advantage. For example, Hooktail eats some of the audience to regain 10 HP, also causing all other audience members to flee, making it impossible to gain any Star Power. In addition, the battle shifts off-stage.

Attacking enemies
While Mario and his partners are battling enemies, they can attack enemies with extra power using various Action Commands. Stylish moves are extra commands to please the crowd more and gain more Star Power.

Guarding
To perform a guard action command, one must press or  when Mario's opponent is about to strike him. Guarding reduces the damage he takes from enemy attacks and help the player resist status effects. The player must time it right, though.

Guard: To perform a Guard move, the player must press to dodge enemy attacks, reducing the damage they do by 1, and also protecting Mario from negative status effects. The player has 8 frames (roughly 2/15 of a second) to guard.

Superguard: To perform a Superguard move, the player must press to dodge enemy attacks, negating the attack completely and sometimes damaging the attacker--generally a Superguard deals 1 damage to an enemy who attacks directly and none to foes who attack at range, but it does deflect Pokeys ranged attacks back at them. The player only has 3 frames (or 1/20 of a second) to superguard, making it more difficult to time than a regular guard.

Star Points
Every time Mario wins a battle, he earns Star Points. The amount he earns from each enemy or boss depends on his current level compared to the enemies he earns them from; as his level goes up, he earns less Star Points from them. If Mario's level is just under, matches or exceeds the enemy's, or reaches the maximum level, 99, he does not earn any Star Points from them at all. When Mario's Star Point Level gets up to 100, the player can choose whether to upgrade Mario's Heart Points, Flower Points or Badge Points. Upgrading HP or FP increases the upgraded stat by 5 and choosing BP raises Mario's BP by 3. Mario stops levelling up at 99. Each stat has its own maximum value, which it cannot be upgraded beyond. For HP and FP, this value is 200, but for BP, this value is 99; however, it is impossible for the player to have all three stats simultaneously be at their maximum value at any one time, since the lack of level ups prevent at least one of the stats to be at its maximum.

Shine Sprites
Much like Paper Mario, there are items found in the overworld of Paper Mario: The Thousand-Year Door that, when collected, allow Mario to upgrade his partners to learn new moves and increase their HP. In this game, Shine Sprites fulfill this purpose. The price of upgrading a partner is always three Shine Sprites. There are 42 Shine Sprites altogether in the game.

The Audience
The Audience determines how much Star Power Mario recovers. It consists of various enemies and allies, and sits and cheers as the group attacks. If Mario or his allies use the Appeal action or a Stylish move, they recover more Star Energy. The audience is even used by various bosses. Hooktail, Cortez, and the Shadow Queen all use the audience to restore their HP. Magnus von Grapple 2.0 can also use members of the audience to attack by launching them at Mario and his partners.

The Audience occasionally takes active participation in the battles; some spectators throw helpful or hurtful items, while others may incapacitate other audience members, making Star Power recovery more difficult.

Bingo!
An icon appears next to Mario's Star Power Gauge whenever the player successfully uses the Action Command of an attack. If the player has two matching icons and if the player executes an additional Action Command, Mario can take the Bingo wheel for a spin.

Items
Items are objects that help Mario and his partners on his journey. Most of them change and heal his stats such as Heart Points (like Mushrooms), Flower Points (like Honey Syrup), Attack (like Power Punch), Defense (like Courage Shell), and some give the player status boosts (like Repel Cape), but some damage the enemy (like Fire Flower) and/or give them status ailments (like Mr. Softener). Mario may hold on to 10 items on his body but he can store 31 items at any Item Shop and withdraw them at any time there. The amount of items Mario can hold is doubled after he collects the Strange Sack.

Badges
Badges are objects that Mario and his partners can use throughout the course of the game. They can be purchased at the Lovely Howz or by Charlieton, traded for Star Pieces by Dazzle, won at the Pianta Parlor or found in one of the places Mario and company visit. The blocks in which badges are found in the field are red in color, unlike normal item blocks which are yellow.

When leveling up, Mario can gain Badge Points (BP) which allow him to use badges he has already found. Some of the badges add new Jump or Hammer moves to Mario's commands during battle and other new abilities.

Badges can also affect Mario and his partners outside of battles. After the battle certain badges can increase the amount of coins, flowers, hearts, or Items enemies drop. Enemies might also carry badges in battle, which only Ms. Mowz can steal right away, and there is a likelihood that they might leave them when they are defeated.

Two special badges, the W Emblem and the L Emblem, can change Mario's clothing. With the W Emblem, Mario gets Wario's clothing, with the L Emblem, he gets Luigi's clothing, and with both Emblems combined, he gets Waluigi's clothing.

If multiple copies of the same jump or hammer badge are worn at once, the FP requirements increases exponentially, whereas the attack power increases linearly.

Enemy formations
In Mario's adventure in Paper Mario: The Thousand-Year Door, he encounters enemies on the field. When he engages battle with them, there are often other enemies that accompany the one that Mario encountered on the field.

Bosses
Bold signifies chapter bosses.

Hidden block locations


In Paper Mario: The Thousand-Year Door, Mario can discover hidden ? Blocks throughout the game. Ms. Mowz is helpful in discovering them. There are 15 invisible ? Blocks in the game.

Selling prices
In Paper Mario: The Thousand-Year Door, Mario can sell items from his inventory to shopkeepers in the item shops in the game. Most items can be sold to the shopkeepers for a set price at every shop, however, some items sell at a higher price depending on the location of the shop and the item itself. Mario can make a profit if he purchases an item at a low price from one store, and sells it to another that buys it from him at a higher price. One Trouble Center trouble exploits this fact.

Star Pieces


During the adventure, Mario and co. can collect Star Pieces by finding them in hidden spots, underneath chambers which he can use the Spin Jump to reveal, and earning them from other characters. Ms. Mowz is useful in finding the overworld Star Pieces. Mario can then trade them with Dazzle for Badges. There are 100 Star Pieces in the game.

Trouble Center
In Rogueport, there is a Trouble Center which offers the citizens' troubles for Mario to solve. An anonymous quest comes from Ms. Mowz and requires Mario to find a badge she is looking for but can not find. After this quest is completed, she joins Mario's team.

Zess T. recipes
Mario first breaks her contact lens in the Prologue. After Chapter 2, Mario bought her a new one, and she returned home. Mario can ask her to cook something. After completing her Trouble Center trouble, she is able to cook two items at once.

The Pit of 100 Trials
The Pit of 100 Trials is an optional challenge. Before or after saving the world, Mario can take on the enemies found in the 100-basement floor area known as the Pit of 100 Trials. The enemies located on levels 51-99 are especially strong. Upon reaching floor 100, Mario discovers Bonetail, the long-lost relative of Hooktail and Gloomtail. After defeating Bonetail, Mario receives the Return Postage Badge.

Similarities to Paper Mario
There are many similarities between the original Paper Mario and Paper Mario: The Thousand-Year Door, including these elements:
 * The opening is identical to that of the previous game, right down to Parakarry delivering a letter from Princess Peach.
 * The first partner of both games is a Goomba that gives Mario hints on both enemies and the area. They both have headbonk, tattle, and multi-bonk as attacks.
 * The second partner of both games is a Koopa Troopa. Both are able to be shot out to hit switches, etc. Both of them are also able to use Shell Toss and Power Shell in battle.
 * Both games have partners obtained in Chapter 3 that have first and last attacks that deal multiple low power hits. Bow with her Fan attacks and Yoshi Kid with his ground pound and Stampede attacks.
 * The fourth partner of each game allows the player to travel across gaps, Parakarry and Yoshi, respectively.
 * Both games have a Bob-omb as a partner, both are able to destroy cracked surfaces, Bombette and Bobbery, respectively.
 * The fifth partner of both games allows Mario to become invisible to enemies, Bow and Vivian, respectively.
 * Both games have a partner who is able to uncover hidden items, and whose basic attack pierces through defense, Watt and Ms. Mowz, respectively.
 * Both games have a partner who has betrayed an enemy to join Mario's party, Lakilester and Vivian, respectively.
 * Both games have a partner who lets Mario to ride them to move faster, Lakilester and Yoshi, respectively.
 * Both games have some way to let Mario traverse through water, the partner Sushie and Boat Mode, respectively. Additionally, both are only available when stepped on a specific panel.
 * The main plot point of both games is to find seven star-shaped entities, each granting Mario special abilities.
 * Both games have an upgrade system for Mario's Jump and Hammer attacks.
 * In both games the player is able to play as Peach between chapters. The player is required to dress Peach up as an enemy to learn secrets. Also, the player can cook something in both games. In Paper Mario: The Thousand-Year Door, Bowser's side-quest is separated from Peach's, as he is not the one who kidnapped her.
 * As with the first Paper Mario game, a main antagonist sees Peach disguised as a minion, and remarks on how she smells "too nice".
 * Mario and Peach contact each other using friendly characters in both games. Twink helped in Paper Mario and TEC-XX in The Thousand-Year Door. In the end, both Twink and TEC develop feelings for Peach (despite of the latter is actually an AI).
 * Mario must solve a mystery in both games. A Bumpty is Mario's fellow detective in both.
 * At one point in the games, Mario falls for a ploy created by the boss of the level which led him to be confined in a cage alongside several other prisoners. A ? block in Paper Mario, and a fake puni pedestal in The Thousand-Year Door.
 * Chapter 1 in both games features a castle/fortress as the location of the boss, with both being located in peaceful, green plains. Additionally, both bosses are revered by denizens of the local town (Koopa Village and Petalburg, respectively, which are both largely inhabited by Koopas). Both towns feature a distinctive, elderly Koopa (Kroop and Koopa Koot, respectively).
 * The partner acquired in Chapter 2 in both games required Mario to bring them an item.
 * An oversized Clubba is the boss of Chapter 3 in both games, and both have a secret that involves making themselves powerful. Both are sought after by persistent female characters interested in finding lost persons (Bow and Jolene, respectively). Additionally, both Clubba characters have positioned security units to guard certain areas (Sentinels and Glitz Pit Security respectively).
 * In both games, at one point, Mario has to chase the Chapter 3 bosses (Grubba and Tubba's Heart).
 * Chapter 4 in both games involves Mario accessing the storage room of a certain shop to make progress. It also involves widespread (and comical) mischief in a town; for Paper Mario, it is the Shy Guy frenzy that takes place. For Paper Mario: The Thousand-Year Door, the denizens of Twilight Town are being turned into pigs at the toll of a bell.
 * Moustafa and Flavio both give the player stones needed to reach an ancient, rumored to be haunted, place. Also both of the ghost bosses (Tutankoopa and Cortez) try to intimidate Mario by uttering threats as he progresses through the level.
 * Buying a Dried Shroom and another certain item along with it was a secret sign in both games that was required to reach Moustafa and Don Pianta, respectively.
 * Chapter 5 takes place on a tropical island with coconuts in both games and both involve an expedition. Also, in both games this is when Mario's oldest partner joins him, and they both have to be rescued from being stuck in a tree before they do so.
 * The Chapter 5 bosses, Lava Piranha and Cortez, are similar as Cortez's spine in his first form and Lava Piranha's stem are in the exact same position, and both of them have multiple forms, each with the same amount of HP. They are also accompanied by multiple entities, each with their own mechanics, attacks, and HP.
 * In both games, Princess Peach must make something. Also, in both games, if she makes a mistake in the directions of making it, it comes out wrong (making a cake for Gourmet Guy and making the invisibility potion)
 * After the battle against Cortez is over, one of the Toad sailors tells everyone that he feels a "slight wind" coming from the cracked wall, just as Misstar did in the first one. The Bob-omb partner of both games is needed to blow that up. Also, the most frequently fought boss of both games (Jr. Troopa and Crump, respectively) conveniently show up after Chapter 5 is completed.
 * Chapter 6 takes place in a beautiful area and has a boss that can do a very high amount of damage when charged up: 16 for Huff N. Puff, 10 for Smorg. Also, both are blob-shaped and made up of a smaller species. Additionally, Ruff Puffs appear in the sixth chapter of both games.
 * Chapter 7 features a snowy region.
 * Chapter 8 includes a battle against Bowser before the final battle. Also, Kammy Koopa is fought in both chapters.
 * Both games contain puzzles in some places that are solved identically or similarly.
 * The Riddle Tower has many puzzles from Crystal Palace, including walking through or blowing up seemingly solid walls.
 * The Palace of Shadow has puzzles and traps from Bowser's Castle, including an area wherein Mario only makes progress by following a pattern (though this is actually taken from the final castle level in Super Mario Bros.)
 * Both dungeons in the final chapters have rooms with stairs where Mario has to defeat B. Bill Blasters to reach the next level.
 * The main villain of both games (which have kidnapped Peach) had to be chased through long stairways in the eighth chapter of both games.
 * Mario's final battle is divided into multiple parts. At one point, each boss is invincible and Peach plays an integral role in negating that invincibility.
 * Peach conveniently gets taken away in both games right before Mario and company reach the hideaways of the games' main antagonists.
 * In both games, there is a scene where Mario can turn into 8-bit Mario with Super Mario Bros. level 1-1 music playing.
 * Both games have Merlon standing outside his house, waiting for Mario and his partners to show up, where he tells them about a dream that he had, and tells them to let him know if they find out the meaning of it. Afterwards, an item that is placed at the top of Merlon's house is revealed.
 * Both games have a spike room where Bow's Outta Sight or Vivian's Veil must be used, and the position of the paths across the spikes are identical.
 * Both games feature a boss who poses a threat by eating people (Tubba Blubba and Hooktail), and both of these bosses have a secret weakness.
 * Both games include a test during the Chapter 5 interlude that Princess Peach has to take and has information that helps Mario in the future.
 * Both games end with a parade led by Luigi (though in Paper Mario: The Thousand-Year Door it is not a traditional parade, and is mainly a line of all the character's silhouettes used as a way to show everyone).
 * Both games' endings feature a scene in which Mario, after returning home from his travels, is shown hanging around with Luigi, having just told his brother the story of his adventure.

Quotes

 * "Omigosh! Is… Isn't that a treasure map?! You HAVE to tell me where you got that!" - Goombella
 * "And with that...pow! I'm gone!" - Lord Crump
 * "Mmmmmmwee hee hee hee! I have no quarrel with you...but I simply can't allow you to hunt for the Crystal Stars." - Beldam
 * "And then I, Grodus, will build a new world! A perfect, ideal world... Yes. A world made by me, about me, and for me! GAAACK ACK ACK ACK ACK!" - Sir Grodus
 * "I'm... I'm sorry Sis. This Mario is the only person who's ever been kind to me..." - Vivian

Title theme

 * The title theme was edited in international versions to flow smoother and make the drumroll more subtle than the Japanese version.

Technical changes

 * There is no health warning screen when starting up the game in the Japanese version.
 * There is no delay for when the player can press start on the title screen in the Japanese version.
 * Holding when the player does not have the Ultra Boots prevents Mario from moving in the Japanese version.
 * On the Level Up screen, the cursor is set to FP by default in the Japanese version, while in the international versions, the player has to manually move the cursor to either HP or BP.
 * In the Japanese version, Mario and his partners are fully healed at the end of Chapter 1, but at the end of all the other chapters, they do not get healed at all. In the international versions​, Mario and his partners are fully healed at the end of each chapter except Chapter 8.
 * The international versions have more Stylish moves than the Japanese version. For example, there is no second Stylish after a normal jump in the Japanese version.
 * Many of the items at the Pianta Parlor have different positioning in the menu in the Japanese version.
 * The backtrace screen has some additional functionality in the international versions. In the international versions, the entire screen is used and also scrolls, while in the Japanese version only a part of the screen is used and it does not scroll.
 * The international versions have a wider frame window when pulling out Action Commands.
 * In the Pit of 100 Trials, when a player defeats an enemy, the pipes show up faster in the Japanese version.
 * Koopook is moved to a different position (further to the left) in Hooktail Castle during his trouble in the Japanese version.
 * Every enemy's stats stayed the same between all versions. However, the American version mistakenly claims that the Red Spike Top has 5 defense instead of 4, and that Rawk Hawk has 3 attack and 1 defense rather than 4 and 0, respectively. These mistakes were corrected in the European version.
 * The English script mistakenly says the Zess Frappe and Icicle Pop restore 20 and 10 HP when they restore 20 and 15 FP in all versions, respectively.
 * During pre-Chapter 5, Swindell the Bandit is moved to the far side of East Rogueport near the barrels. In the international versions, there is one less barrel, and Swindell's position is slightly altered.
 * Giving Lumpy 200 coins early in the game leaves Mario with 500 coins later in the Japanese version and 600 coins later in international versions.
 * All Fuzzies have horrible vision in the Japanese version, as they often do not even notice Mario when he goes by them. In the international versions, the Fuzzies have better vision and thus notice Mario more quickly. In addition, the Fuzzies move slower in the international versions.
 * There is no slowdown when moving up slopes on rooftops with Yoshi in the Japanese version.
 * At the end of Bowser's levels, fireworks are fired in the Japanese version but not in the international versions.
 * In the original Japanese script and every other translation of the game, the final RDM email features an additional "hidden" section if the player scroll downs for an extended period of time. This portion was removed from the English translation, despite retaining the statement hinting at its existence.

Area changes
Several areas had some changes made between the Japanese and international versions.

Prologue

 * The X-Nauts who jump on Mario in the Prologue move faster in the Japanese version.
 * In the Japanese version, the moving platforms in the Rogueport Underground (the one in the first area and the two in the room with the pipe to Petal Meadows) do not move as far to the left and right as the ones in the international versions.

Chapter 1

 * Question #2 of the Thwomp quiz in Shhwonk's Fortress asks for the price of a Mushroom and a Fire Flower in the Japanese, French, German, Italian, and Spanish versions, as opposed to the price of a Mr. Softener and a Fire Flower in the English version. However, in the US Paper Mario: The Thousand-Year Door demo included in the Nintendo GameCube's Demo Disc Version 18, this question asked for the price of a Mushroom and a Fire Flower like in the other versions.

Chapter 2

 * In the Japanese version, the right Pale Piranha on the screen where the Shadow Sirens are fought in Boggly Woods acts differently from the one in the international versions.
 * In the Japanese version, when unlocking the blue cage door in the Great Tree, the game checks for and removes the Strange Sack from Mario's inventory if he has it (which permanently prevents it from being obtained again as there is only one in the game). This does not happen in the international versions. Also in the Japanese version, after unlocking the blue cage door, there are several frames where Mario is able to move around freely.
 * In the Japanese version, Punio's textbox when he thinks about how to reveal the secret entrance advances automatically instead of manually.

Chapter 3

 * In the Glitz Pit, all fights (excluding ones that start with special cutscenes, such as The Goomba Bros. and The Armored Harriers) start about 2 seconds faster in the Japanese version when compared to the international versions.
 * In the Japanese version, when returning to Rogueport from Glitzville, the entire cutscene is about 7 seconds longer than in the international versions.
 * During Peach's section right after Chapter 3, when leaving the dressing room to return to TEC after talking to Grodus, the player can move while the door is opening in the Japanese version.

Chapter 5

 * In the Japanese version, Mario can get the Keel Mango from the trees at Keelhaul Key at any time. In the international versions, the chapter must be completed first. This was most likely changed to ensure that Flavio ends up getting the Coconut rather than the Keel Mango as both items are tropical food and giving Flavio any food item that is not a Coconut results in him asking for something more tropical.
 * One Flower Fuzzy on the screen with the blue pipe in Keelhaul Key was removed in the international versions.
 * The Flower Fuzzy on the screen with the two Putrid Piranhas continues to move around if it falls down in the Japanese version, while it stays still in the international versions.
 * In Pirate's Grotto, the chest behind the waterfall contains a Damage Dodge P in the Japanese version. In the international versions, this is a Defend Plus P.
 * In the black chest room in Pirate's Grotto, when Mario defeats the Embers, the key randomly falls to the left or right in the Japanese version. In the international versions, it simply falls straight down.

Chapter 6

 * On Day 3 of the Excess Express, Mario gets an email in the dining car in the Japanese version. In the international versions, Mario gets this email to the right of his room.
 * When the Smorgs appear when talking to the Engineer, they do not cover the right part of the window in the Japanese version.
 * In the outside room at Riverside Station with the Poison Pokeys and Ruff Puffs, there is a block that can be jumped on to hit a hidden block that contains a Thunder Rage. In the Japanese version, this block is a breakable block, and breaking it causes it to stay broken until the player leaves Riverside Station. The international versions made this block unbreakable.

Chapter 7

 * X-Naut Fortress's third puzzle room has a safe path two squares long in the Japanese version and three squares long in the international version, thus slightly reducing its difficulty.
 * On the moon, on the screen with the pipe, blowing up the rock containing the pipe causes a small cutscene to play in the Japanese version. This cutscene does not occur in the international versions.

Chapter 8
The changes made consist of the fight against the Shadow Queen:
 * In the Japanese version, none of the Shadow Queen's attacks can be superguarded against.
 * During the first phase of the Shadow Queen fight, she changes to her true form after dealing at least 39 damage to her in the Japanese version. In the international versions, this happens after dealing at least 61 damage.

Aesthetic changes

 * Some items were redesigned in international versions:
 * Super Luigi 5 is red instead of orange.
 * The kanji on the Wrestling Mag is replaced with scribbles.
 * The Power Rush badge has a different letter for every language.
 * Vintage Red was renamed Chuckola Cola and recolored purple to resemble soda instead of wine.
 * The Boos Peeka and Lahla wear bunny ears in the Japanese version, but cat ears in international versions to avoid resembling a.
 * TEC-XX's camera "eye" is blue instead of red in international versions to tone down similarities to the.
 * Larson's Toad chalk outline and bloodstains in his house were removed from international versions to remove violent undertones.
 * In the English and German scripts, Vivian is referred to with feminine pronouns and has no mention of being a male-to-female.
 * The Shadow Queen is slightly more formal and condescending in the English script.
 * Before the battle against Shadow Queen, if Mario chooses to be her servant, after her spell has casted on Mario, Mario's sprite changes to the same as Doopliss's appearance when impersonating as him in the Japanese version, notably for the evil-looking appearance, and the effects from L Emblem and W Emblem are also removed (like how Doopliss's fake copy of Mario cannot change colors either). However, in the international version, Mario keeps the same angry pose before the spell, and his appearance and color remain unchanged.
 * A few cutscenes involving flashing lights were edited down in the international versions, probably to reduce the chance of players getting epileptic seizures:
 * The flashing lights during the first Shadow Queen cutscene were reduced.
 * The flashing lights during the cutscene in the room that makes the Emerald Star appear were reduced.
 * However, the animation for Showstopper, which despite being arguably worse than the two stated above, was not edited.
 * PAL versions have additional differences from all NTSC versions. Only NTSC versions can be played in progressive scan mode, and only PAL versions can be played in 50Hz mode, using the same method to activate each. The American and Japanese versions have their languages locked to English and Japanese, respectively, while the PAL version can additionally be played in Spanish, French, Italian and German depending on the GameCube settings. Also, in NTSC versions, Mario has two different talking animations, one involving him raising his hand and one involving him moving his mouth, and each one is used in different scenarios. Only the "mouth moving" one is used in the PAL version, however, to avoid resemblance to the Nazi salute.

Reveal trailer
This game was initially titled Paper Mario 2 and featured a far different logo, one reminiscent of the original Paper Mario's logo.

Part of the original trailer shows an extra ledge above the pipe in the room directly east of the Thousand Year Door, with an HP Plus badge on it. It could be accessed via a moving platform which had a wall over it halfway, which appeared to be passable with help from Vivian. Also, Beldam and Doopliss were originally going to be fought somewhere in Riverside Station. The trailer also showed that Item Shops would be labeled with Mushrooms, much as in Super Paper Mario, rather than the Fire Flowers seen in the final game. Red Bones was initially named "Red Koopa Skeleton." In the same trailer, one can see that "Tornado Jump" was initially called "Hurrican Jump". [sic] The status element Slow had a different icon, a snail instead of a sad purple face.

Koops splashing on Dry Land
At the dock of Rogueport, the player should stand on or near the bollard and use Koops's ability, holding so he remains in place. Without letting go of the button, the player should walk away so that Koops is offscreen, and talk to a character in the same area. When the player is done, Koops respawns next to Mario. There is a splash animation even on dry land. This glitch also works in Petalburg.

Staff
Intelligent Systems developed the game with Nintendo publishing it. The music is credited to Yoshito Hirano and Yuka Tsujiyoko.

Reception
Overall, Paper Mario: The Thousand-Year Door received very positive reviews from critics, who praised its nuanced story, characters, and humor, in addition to its battling system, multiple side-quests, and soundtrack.

In 2019, a petition on was started to get Paper Mario: The Thousand-Year Door remade in HD.

References to other games

 * Donkey Kong: One of the badges is named "Jumpman", referencing to how Mario was alternatively named in this game. In addition, although not in the game itself, the Official Nintendo Power Player's Guide alluded to Mario's encounters with the titular ape from the game where they mentioned that the X-Nauts thought they could dissuade Mario with various platforms at high places, but they had not heard of his exploits against "a certain ape."
 * Super Mario Bros.: At the X-Naut Fortress in the Changing Room, Mario and Co. can change into an 8-bit sprite of themselves, along with the Super Mario Bros. music playing in the background. Hamma also mentioned that his grandfather was at World 7-1. Bowser's gameplay is also a direct parody of this game. In the Japanese and French versions of the game, the video-game obsessed Toad from Petalburg refers to Super Mario Bros as his favorite game for the Famicom and Nintendo Entertainment System, respectively, also urging Mario to play it in the latter version.
 * Famicom Disk System boot up: During the Peach transition scene for Chapter 5, when Peach is invisible and retrieves a disc from Grodus's office, the computer screen displays a scene of Mario and Luigi fighting over a light switch, referring to the boot up screen for the Famicom Disk System if the player did not input a disk beforehand.
 * Super Mario Bros. 3: The Grass Land theme is arranged as part of the music that plays during the opening cutscene. Whenever Jolene (while under the alias of "X") sent Mario an e-mail, the Ice Land map screen theme would play. The music that plays when Mario is riding the blimp is a cover of the athletic theme from this game. This game also included Boomerang Bros., Fire Bros., and Boos, which originated from this game. Also, the "king saved" music can be heard in Luigi's story telling theme. Also like Super Mario Bros. 3, the game's story is implied to be a stage play (although it is more direct than in the former game, as it was only stated by Shigeru Miyamoto in the former case). In addition, Peach after each chapter ends up sending (e-)mail to Mario with advice for the next level, with her final mail upon completing all objectives being intercepted by the main villain, similar to in Super Mario Bros. 3. Bowser's theme song contains a cover of the castle theme.
 * Super Mario World: Whenever Peach sends Mario an e-mail, the title screen theme would play. Whenever Mario gets an e-mail from other people, part of the epilogue theme (from when a Koopaling castle is beaten) plays. When Mario wins a battle, the "level clear" sound plays.
 * Super Mario World 2: Yoshi's Island: Blue Bandits appear as NPCs. Atomic Boo closley resembles Bigger Boo from this game.
 * Super Mario 64: In the first Princess Peach interlude, Peach is singing the Inside the Castle Walls theme from this game when she is in the shower.
 * Paper Mario: Parakarry makes a brief cameo at the beginning of the game, and delivers a letter to Mario from Peach, just like the previous game. Lady Bow also makes a cameo appearance, and makes a direct reference to Boo's Mansion, as well as the adventure they had. There is also a random Toad at the Excess Express (after Chapter 6 is completed) that asks Mario a quiz question, ("What did Bowser steal in the first Paper Mario?"), and the answer is, "Star Rod". The video game-obsessed Toad kid from Petalburg also mentions that he has been playing the game, describing Bow as the "cutest Boo of ALL TIME!!!" Jr. Troopa also appears in the background in the picture that Zip Toad attached to his e-mail. Gulpits are also given a reference when Grubba exclaims, "GREAT-GALLOPIN' GULPITS!". A Ratooey at Rogueport Harbor who went on a quest for oil in Dry Dry Desert can tell Mario about this adventures at the end of the game. Every part is a chapter of Paper Mario game. In the email he sends to Mario after finding him, Koopook says he is now hiding in Crystal Palace in the Japanese version; however, this last reference is lost in the English translation, as Crystal Palace is instead translated as "Goomstar Temple". Kolorado was a student of Professor Frankly, and the former's deceased father appears as a crumpled Dull Bones in Hooktail's Castle, which Koops confuses for his own father. One of the houses in Poshley Heights has a model of the K64.
 * Mario Kart: During one of Luigi's stories, he tells Mario he had to sign up for a Kart race, and mentions he had driven karts before, giving reference to the Mario Kart series.
 * Luigi's Mansion: A crow in Twilight Town says he will set up an estate pay site named Luigi's Mansion, and his crow friend says that "he's heard that name somewhere before", referencing this game.
 * Super Smash Bros. Melee: In the Spanish version of the game, Rawk Hawk's victory gloat after beating The Koopinator specifically referenced Super Smash Bros. Melee (in all other versions, he simply says they are better off playing video games without naming one in particular).
 * Super Mario Sunshine: Toadsworth, Piantas, and Shine Sprites appear in the game to upgrade Mario's partners. The parrot in Creepy Steeple randomly says the infamous translation of "Shine get!".
 * Mario & Luigi: Superstar Saga: Chuckola Cola is an item in this game, referring to the game it has been appeared first. The "Super-Guarding" ability was likely inspired by the ability to counter enemies' attacks in Superstar Saga. Mario gaining field abilities to use in battle (Spin Jump, Spring Jump, Super/Ultra (spin) hammer) as special FP consuming attacks were also likely inspired by field abilities in Superstar Saga being used in battle as Bros. Attacks. One of Bowser's options during his conversation with Pennington during the Chapter 7 interlude is The Shadow Thief, a reference to Popple. The difference of the naming methods between the English and Japanese titles are similar to this game, as the English titles of both games have a subtitle under the series names (Mario & Luigi and Paper Mario respectively), while the Japanese titles simply have the term "RPG" under the series names.

References in later games

 * Super Paper Mario: This game is alluded to by a video game-obsessed Toad in Petalburg. At the end of the game, he states that he has been playing "the new Paper Mario game" called Super Paper Mario, which was released in 2007 for the Wii, and that it will be pleasing to fans of Luigi, which hints that the game was already in production and/or planning stages at the time Paper Mario: The Thousand-Year Door was in development. All seven partners from Paper Mario: The Thousand-Year Door make cameo appearances as Catch Cards that are won by completing the Duel of 100 at Sammer's Kingdom. Francis also has plush toys of the Yoshi (in all colors), Vivian, Bobbery, and Pennington, along with a poster of Petuni. In Francis' list of things to buy, Rawk Hawk was given a reference when he stated that he wants a DVD called, "Harder than Bedrawk: The Rawk Hawk Story". Francis also stated that he wants a Ms. Mowz doll with "real-smooching action", an Excess Express train set, and a Magnus Von Grapple action figure. Francis also happens to watch "Starship X-Naut" and "The Grodus Chronicles". Also, Fracktail and Wracktail, themselves are homages to Hooktail and Bonetail. Additonally, there is also a Sammer Guy who calls himself "Laughing X-Naut" and another who calls himself "The Thousand Year Roar". Lastly, Slim's ability to make Mario, Peach, Bowser, or Luigi thin is a reference to the second curse in Paper Mario: The Thousand-Year Door.
 * Super Smash Bros. Brawl: Goombella, Mini-Yoshi, Vivian, and Rawk Hawk appear as Stickers. Goombella also has her own trophy. Also, the words, "CRUMP" and "RAWK" appear in the random name selection, which are possible references to Lord Crump and Rawk Hawk.
 * Paper Mario: Sticker Star: In the level Shy Guy Jungle, there is a pile of garbage with many letters, one letter is written by Goombella and it states: "Observations on the Ancient Civilization of the Chomp Ruins."
 * Super Smash Bros. for Nintendo 3DS: The S.S. Flavion appears as a variation of a Paper Mario stage in this game. A Big Blooper based on the boss also appears in the stage variation's background. An arrangement of the Rogueport theme is also part of the stage's main song.
 * Super Mario 3D World: The Fuzzy Horde, which debuted in this game, returns in several levels.
 * Mario & Luigi: Paper Jam: Paper Mario's Airplane and Paper Modes return. During Trio Grab, Paper Mario turns into a tube, similar to Tube Mode. He can also turn into a paper drill during Trio Drill, which is similar in concept to the paper abilities from this game. When Paper Mario meets the Mario Bros., he performs a Spring Jump. Paper Mario borrows his blocking and KO'd animations from this game. The trio gains Star Points by performing Action Commands correctly, which is similar to how Paper Mario and his partners had to appeal to the audience by doing the same thing, and by also being stylish. The stage where Mario, Luigi and Paper Mario stand when they level up is similar to the stage from this game's battles, down to the yellow stripes on the curtains.
 * Paper Mario: Color Splash: Peach summons Mario over to the current destination due to a discovery she made (although in this case Peach personally has Mario come along). Peach also ended up abducted shortly after bringing Mario along (although in that case, Mario does witness Peach's abduction). She also sends mail giving some hints about the main villain's plan and the next destination that Mario should head towards in the form of Holo-Peaches, and her last mail has Peach's message being cut off by the main antagonist (Black Bowser) just as Peach was about to give key details about his villainous plan. In addition, a character gets possessed by a grave evil (in this case, Bowser via Black Paint, while in Paper Mario: The Thousand-Year Door, it was Peach who was possessed by the Shadow Queen). Also, the Big Paint Stars serve a similar function to the Crystal Stars.
 * Paper Mario: The Origami King: Peach's design from The Thousand-Year Door appears as a photo. Additionally, when Mario and Bob-omb interact with the steering wheel on the Princess Peach, the latter mentions that he dreams of being an admiral someday, in reference to Admiral Bobbery.