Paper Mario: The Thousand-Year Door

Paper Mario: The Thousand-Year Door (known as Paper Mario RPG in Japan) is the second installment in the Paper Mario series, with the first being Paper Mario. It was released for the Nintendo GameCube in 2004.

The plot of the game revolves around Mario, who embarks on a mission to collect the seven Crystal Stars in order to open the Thousand-Year Door. After learning that Princess Peach has been kidnapped, he also sets out on a mission to rescue her from the X-Nauts. The game has intermissions between each chapter, in which the player assumes the role of Bowser, as well as Peach, who have their own stories that complement the main plot.

Prologue: A Rogue's Welcome
The adventure begins when Princess Peach goes on a cruise to Rogueport. After arriving, she meets a hooded woman, and buys a box. She finds a map inside of it, and sends it to Mario. Soon after that, she is kidnapped by Sir Grodus. Mario receives the map and boards a ship to Rogueport.

After Mario reaches Rogueport, he finds Goombella being harassed by Lord Crump. After defeating the X-Naut general and escaping from the X-Nauts, Goombella introduces herself, and Mario explains his quest. Goombella tells Mario to go to Professor Frankly's house and show him the map; the professor then explains the legend and the Thousand-Year Door. The three then enter the sewers, and they encounter a mysterious Black Chest Demon, who "curses" Mario, giving him a new ability. Mario uses this power to reach the Thousand-Year Door and holds the map in the air, revealing the location of the first Crystal Star.

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Chapter 1: Castle and Dragon
Mario and Goombella show the map to Professor Frankly, who reveals that the castle upon it is in the same vicinity as Petalburg. The group passes through Petalburg discovering Hooktail and passing Shhwonk Fortress on their way to Hooktail Castle, getting Koops as a new member. With the help of Ms. Mowz and after gaining another ability from a Black Chest Demon, they encounter Hooktail and defeat her, receiving the Diamond Star.

Somewhere else, Princess Peach is revealed to be kidnapped by the X-Nauts. When an X-Naut tells Sir Grodus someone nabbed the first Crystal Star, Peach accidentally blurts out Mario's name. Grodus hears this and orders Shadow Sirens to steal the map. Peach soon meets TEC 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 and Peach, and then he decides to leave to 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 and reveal the location of the next star.

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Chapter 2: The Great Boggly Tree
The second Crystal Star is revealed to be in The Great Tree in Boggly Woods. With the help of Punio in Rogueport Sewers, the group reaches the Boggly Woods. 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. After realizing 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 doesn't 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; with the aid of a special orb and after defeating the Jabbies, they get the second star. There, Lord Crump snatches it, and activates a five minute 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 calls for the Princess, and asks her to dance with him. TEC then lets Peach e-mail Mario. Meanwhile, Bowser and Kammy are in Petal Meadows. Bowser spots Peach, and starts talking to her, only to find out it was a poster.

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 next Crystal Star, and they visit the Prof. for details.

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Chapter 3: Of Glitz and Glory
The third Crystal Star appears on a large arena in 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 and spot the Crystal Star on the Champ's Belt, held by Rawk Hawk, the current champion. They sign up as a team, 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 reveal 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. spot him and chase him into the arena, where he transforms into Macho Grubba. The group manages to defeat him. After the fight, Jolene, Grubba's assistant, appears and reveals herself as the mysterious X, explains her story, and gives Mario the star.

At the X-Naut base, TEC 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 is searching for one of the Crystal Stars in the Great Tree. Kammy Koopa and the Puni Elder get into a fight, and the Puni Elder mentions that "Marty-o" already has the Crystal Star.

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

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Chapter 4: For Pigs the Bell Tolls
The Prof. tells the group that the Crystal Star is located in the Creepy Steeple near a small town named 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 attack 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 "Mario". Meanwhile, the real Mario returns to Twilight Town, and meets Vivian. They discover that the monster's name is Doopliss; after guessing his name, Mario chases him and they fight once more. The two defeat Doopliss and reclaim the Ruby Star.

At the X-Naut base, TEC asks the Princess to participate in a sort of "quiz show" with him. By doing this, she discovers the true "treasure" of the Thousand-Year Door. The Princess then sends this news to Mario. Meanwhile, Bowser continues his quest for Crystal Stars by flying up 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 a message from Peach. They reveal the next Crystal Star and visit Prof. Frankly for details.

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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, with the help of Flavio and Admiral Bobbery, they sail to the island with some Toads 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 shipwrecks 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 found out that he was just 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 a battle, Cortez gives Mario his Sapphire Star. Afterwards, Lord Crump abandons his disguise and tells Mario that he will continue attacking him 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 wishes to gain access to a disk at 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. Meanwhile, in Twilight Town, Bowser and Kammy Koopa run into Lord Crump. The three get into an argument. However, Bowser inadvertently ignites the Superbombomb, destroying both armies.

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

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Chapter 6: 3 Days of Excess
The sixth Crystal Star is in the Poshley Sanctum of Poshley Heights. The only way to reach the town is on the famous Excess Express. After doing Don Pianta another favor, he gives Mario the ticket. Once on the Excess Express, Mario and his team on the first day found many mysterious happenings, including thefts, threatening messages, and the dangerous Nitro Honey Syrup. With the help of Pennington, a penguin detective, they manage to solve the crimes, capturing a fake Zip Toad who was really Doopliss in disguise. On their second day of travel, a stop at Riverside Station is necessary, and Doopliss escapes, and the drawbridge has been lifted, preventing the Excess Express from continuing its route. The gang enter Riverside Station and flip the switch to bring the drawbridge back down. They discover that a group of Smorgs are behind it. The next day, a Smorg Miasma attacks the train. After Mario and his friends defeat the creature, rescue the passengers, and finally reach Poshley Heights. They venture into Poshley Sanctum, a museum that happens to belong to Pennington. The Shadow Sirens are already inside, and snatch what appears to be the Garnet Star, on display on a podium in the rear of the museum and escape. However, Pennington reveals that what they stole was a fake, and lets Mario find where the real Star is. After some exploring, Mario and friends found the real Garnet Star.

Back at the X-Naut base, the X-Nauts tell Grodus that Mario has six of the seven Crystal Stars. 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 the data-wipe procedure. 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, but most of it is cut off due to TEC being deleted. Back in Rogueport, Mario and co. reveal the next Star's location and visit Prof. Frankly for details.

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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 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, Lord Crump appears, bragging about his latest creation — Magnus von Grapple 2.0. 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, they discover that all of the doors have locked. The heroes later find TEC, who barely survived Grodus's order to purge his databanks. He recognizes Mario and tells him to rescue the Princess, activating an emergency transporter. The group is transported to a room in Rogueport Sewers. After exiting the room, Prof. Frankly meets them at the entrance and urges them to open the Thousand-Year Door.

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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.

The Palace itself is full of enemies, puzzles, and traps. Eventually, the group discovers a black dragon named Gloomtail, older brother of Hooktail. After being defeated, he relinquishes the key to the Riddle Tower. After solving the puzzles of the Tower, the group fights the Shadow Sirens once again, and discovers that the "Professor Frankly" that told them to open the door was actually Doopliss in disguise. After defeating the Shadow Sirens, Mario reaches the Throne Room, where he finally finds Sir Grodus, whom he defeats. Bowser and Kammy, who drop in unexpectedly, also battle Mario. Grodus uses this distraction to bring the Princess into the deepest part of the Palace. There, he opens a sealed coffin and frees the Shadow Queen. 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, supposedly killing him. The Queen then possesses Princess Peach, using her as a vessel to sustain her life. The world is covered in darkness. Mario and his allies fight the Queen, but the Queen eventually decides to fight in her real form. She proves too much power for the group, becoming immune to their attacks. Suddenly, the Crystal Stars react to the evil of the Queen and fly throughout the world, each returning to where they were found. And all the hopes help the group break through the Queen's invulnerability. Empowered, the heroes destroy the Shadow Queen, saving the world. The heroes celebrate their happy ending and Professor Frankly reveals that the treasure behind the Door was a Dried Shroom, After saying their goodbyes, Mario and Peach leave Rogueport.

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 Kid 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 arrives with another treasure map.

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Gameplay
In terms of gameplay, 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.

Paper Abilities
Paper Mario: The Thousand-Year Door brings up new gameplay elements not present in the original Paper Mario game. Throughout the game, Mario finds four 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. With the first ability (called Plane Mode), Mario is able fold himself to a paper airplane at certain spots, allowing him to fly over large gaps. The second ability (called Paper Mode) allows him to turn sideways, making him as thin as paper, so that he can get through very narrow passages. With the third ability (called Tube Mode), Mario can roll himself up, allowing him to roll through low passages. With the fourth ability (called Boat Mode), he can fold himself to a paper ship at certain docks, allowing him to move over water. It is noticeable that, to use Tube Mode, Mario has to activate Paper Mode first, and then roll himself up.

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.

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 will fall, damaging all characters on stage and possibly making them Dizzy, the audience helps Mario gain Star Power and also may throw items on stage, 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 the Action Command. Stylish Moves are extra commands to please the crowd more and gain more star power.
 * Countdown: Tilt and hold left, then release when the red light flashes.
 * Tricky Timing: Pressing just before landing on Mario's opponent.
 * Aiming: Aligning a cursor in the center of the targeting reticule
 * Button Mania: Holding on to or repeatedly tapping a button or input an entire sequence.

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 will have a 1/2 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 will only have a 1/4 second to superguard, making it more difficult to time than a regular guard.

Star Points
Every time Mario wins a battle, he'll earn Star Points. When Mario's Star Point Level gets up to 100, he'll choose whether to upgrade his Heart Points, Flower Points or Badge Points. Choosing HP and/or FP will raise Mario's HP or FP by 5 and choosing BP will raise Mario's BP by 3. Mario stops levelling up at 99; however, it is very hard to reach this level because, starting from level 1, the Star Point Value for every enemy decreases by one with each level up. However, for every single battle, the player will always get at least one Star Point, unlike the first Paper Mario, where the player will never get any more Star Points after level 27.

Shine Sprites
When Mario and co. collect Shine Sprites, Mario can give 3 of them to Merlon and Merlon will power up Mario's partners, increasing their HP and teaching them new moves. Getting the Up Arrow in Hooktail Castle will cause Merlon to remember he has an Ultra Stone which will allow Mario to power up his partners a second time, and Merlon will teach Mario's partners ultra-rank moves.

The Audience
The Audience determines how much Star Energy 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 will 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 will appear 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.

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 when he or she joins the party, learns the third after being upgraded to Super Rank, and masters the final move after attaining Ultra Rank.

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 gives the player Status Ailments (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 will be doubled after he collects the Special Item Strange Sack.

Badges
Badges are what Mario may need throughout 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 points defeated enemies leave. Enemies might also carry badges in battle, which only Ms. Mowz can steal right away, and there's a likeliness that they might leave them when they're 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 will increase, but so will the attack power.

All badges found in RPGs like Paper Mario: The Thousand-Year Door are listed here in detail.

Bestiary (Tattle Log)
See the Bestiary for a list of all enemies found in Paper Mario: The Thousand-Year Door, as well as Tattle information provided by Goombella. See the below section for a list of bosses.

Trouble Center Side Quests
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.

Bosses
Yellow signifies chapter bosses.

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
There are many similarities between the original Paper Mario and Paper Mario: The Thousand-Year Door, including:
 * 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 will give 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 will be 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 several, low power hits. Bow with her Fan attacks and Yoshi Kid with his ground pound and Stampede attacks.
 * The fourth partner of each game will allow 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.
 * Both games have a partner that 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.
 * Both games have a partner who has betrayed an enemy to join Mario's party, Lakilester and Vivian, respectively.
 * The main plot point of both games is to find seven stars.
 * 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 TTYD, 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 in The Thousand-Year Door. In the end, both Twink and TEC develop feelings for Peach.
 * Mario must solve a mystery in both games. A Bumptie is Mario's fellow detective in both.
 * In one point of the games, Mario falls for a ploy created by the boss of the level which led him to be confined in a cage. 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.
 * The partner acquired in Chapter 2 in both games required Mario to bring him or her an item.
 * An oversized Clubba is the boss of Chapter 3 in both games, and both have a secret that involves making themselves powerful.
 * In both games, at one point, Mario has to chase the Chapter 3 bosses (Grubba and Tubba's Heart).
 * 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.
 * 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.
 * In both games, Princess Peach must make something. Also, in both games, if she makes a mistake in the directions of making it, it will come out wrong (Making a cake for Gourmet Guy and making the invisibility potion)
 * After the battle against Cortez was over, one of the Toad sailors will tell everyone that he feels a "slight wind" coming from the cracked wall, just as Misstar did in the first one. Also, the Bob-omb partner of both games is needed to blow that up. Also, the most frequently fought boss of both games 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.
 * 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. music playing.
 * Both games have Merlon standing outside his house, waiting for Mario and his partners to show up, where he'll tell them about a dream that he had, and will tell them to let him know if they find out the meaning of it.
 * 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 will help Mario in the future.
 * Both games end with a parade led by Luigi (though in Paper Mario: The Thousand-Year Door it's not really a parade, and is mainly a line of all the character's shadows used as a way to show everyone).

References to Other Games

 * 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.
 * Super Mario Bros. 3: Whenever Jolene (while under the alias of "X") sent Mario an e-mail, the Ice Land map screen theme would play. This game also included Boomerang Bros., Fire Bros., and Boos, which originated from this game. Bowser's theme song is a remix of the background music that plays in castle levels.
 * 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) will play. When Mario wins a battle, the "level clear" sound will play.
 * 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 will ask 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's 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.
 * 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
 * Mario & Luigi: Superstar Saga: Chuckola Cola is an item in this game, referring to the game it has been appeared first. Flavio resembles the Beanbean Kingdom residents, and also carried a bottle of Chuckola Cola with him. Also, two characters named Podley and Podler, are from the Beanish species. Also, the "Super-Guarding" ability was likely inspired by the ability to counter enemies' attacks in Superstar Saga.
 * Luigi's Mansion : Occasionally, Luigi will have the Poltergust 3000 on his back when in the audience. This does not affect anything, though. A crow in Twilight Town also 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", a reference to this game. Another reference is when Mario releases the Boos in Creepy Steeple. One of the Boos asks how many Boos just came from the box, and one of the answers Mario can give is 50. 50 is the total number of Boos that are released by Luigi in Luigi's Mansion.
 * Super Paper Mario: This game is aluded to by a video game-obsessed Toad in Petalburg. At the end of the game, he'll state that he's been playing "the new Paper Mario game", 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. Super Paper Mario was released in 2007.

References in Later Games

 * Super Paper Mario: 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, 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's 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.

Trivia

 * All of the partners from the first Paper Mario were originally going to make cameo appearances in this game, but were scrapped from the final product for unknown reasons. However, Parakarry and Lady Bow do remain in the game, and make appearances at the beginning and in Poshley Heights after completing the game, respectively.