In the field, players control Mario by moving him through the game world and navigating through menus. Menus also control battle, although players can increase their chances of winning a battle through timed presses of certain buttons. Mario in this game is voiced by Charles Martinet.
Mario's adventure begins when Princess Peach sends him a letter with a treasure map enclosed. She requests that he join her on vacation in Rogueport and help her find the treasure indicated by the map. When Mario arrives, he finds the princess missing. After meeting Goombella and Professor Frankly, who believe that following the map will lead them to Princess Peach.
- During Mario's quest to find the Diamond Star, he joined forces with Koops, a Koopa who believed that his father had been killed by Hooktail the dragon. With Goombella, Mario and Koops defeated the dragon and reclaimed both the Star and Koops father.
- Traveling to the Boggly Woods to find the Emerald Star, Mario found the X-Nauts undergoing an enormous search mission for the star. With the help of the Punies (small bug like creatures) and Flurrie, a wind spirit, Mario was able to find the Star and chase the X-Nauts out of the woods.
- At some point in time, the Gold Star came to reside in Glitzville, a floating city that thrived because of the Glitz Pit, a fighting arena. Mario entered the contest in hopes of finding the star, and with the help of a Yoshi friend, discovered that Grubba, the manager of the battles, had been using the Crystal Star to buff himself up.
- When Doopliss, a monster famous for his ability to alter his appearance and the appearances of others, moved into the Creepy Steeple, he found the Ruby Star hidden there. When Mario came looking for it, Doopliss stole Mario's body and name, but with the help of the ex-Shadow Siren Vivian, Mario was able to take his body, name, and the Crystal Star back.
- The pirate ghost of Cortez possessed the Sapphire Star. Following the map to Keelhaul Key with the help of Flavio, a merchant, and Bobbery, a famous navigator, Mario and friends found themselves shipwrecked when they were attacked by ghosts. With Bobbery's explosions to help him, Mario went deep into Cortez's lair. After fighting him, Cortez decided to voluntarily give up the Crystal Star.
- Mario’s next goal was to find the Garnet Star in Poshley Heights. The hardest part would have been getting a ticket fot the Excess Express, the only way to get there, from the Pianta Syndicate, but because of the Shadow Siren’s interference, Mario and friends were faced with roadblocks and Doopliss disguised as a famous celebrity. They may also have lead the Smorg’s attack on the train as well. After arriving in Poshley Heights, Mario was simply given the Star.
- The final Crystal Star was the Star held by the X-Nauts. With the help of the Bob-ombs of Fahr Outpost, Mario and friends launched themselves to the moon and proceeded to storm the fortress. Although they were too late to save Princess Peach, they were able to take the last Star from Lord Crump.
After gathering together all seven of the Crystal Stars, Mario was tricked into opening the Thousand-Year Door by Doopliss, who was disguised as Professor Frankly. Ultimately, after defeating Gloomtail, The Shadow Sirens, Grodus, Bowser and Kammy Koopa, Mario took on the Shadow Queen, who had tricked Grodus in order to possess Princess Peach and thus return from beyond the grave.
While Princess Peach was in Rougeport waiting for Mario to come she wandered into the east side of the town. There she was kidnapped by the X-Nauts until she had given information. The greatest supercomputer in the world was watching this happen in the X-Nauts' lair. He opened the door to Peach's room and summoned her into the computer room. He then fell in love with her and made her do various tasks in exchange for the ability to send Mario messages.
A professor in archeology at Goomba University, he taught both Kolorado and Goombella. While living in Rogueport to research the ancient ruins underneath the town, he was overjoyed to assist Mario and Goombella on their quest to find the Crystal Stars. Throughout the game his is a source of information for Mario and friends, unearthing the ancient legend about the Thousand-Year Door and researching how to get to the locations described on the magical map. His Japanese name, Furankuri, is a combination of Frankly and Kuribo, the Japanese name for Goomba.
Bowser has many cutscenes in which he is a playable character. These involve gameplay and level set-up similar to the original "Super Mario Bros." game for the NES. Remixed music from the original 1985 Super Mario Bros. game is also included. He is voiced by Scott Burns.
When Bowser found out that Princess Peach had been captured by the X-Nauts, he was infuriated, as kidnapping her is his claim to fame. Mario was going after "treasure" (the Crystal Stars) and the princess, leading Bowser to jealousy. Thus, Bowser and Kammy set off to make life harder for Mario and the X-Nauts.
Bowser's journey in the game follows a similar pattern to Mario's. However, he is usually a few steps behind Mario and his friends, so he is met with little success. There are three sections of the game in which you control Bowser through the above-mentioned side-scrolling levels, and several others where you control Bowser similarly to how Mario and Peach are controlled. During Mario's mission in Glitzville, the Koopa king attacks him in the ring and loses. During the last part of the game, Bowser and Kammy Koopa break into the Palace of Shadow, accidentally saving Mario from Grodus. However, Bowser and Kammy attack, allowing Grodus to regain consciousness and take Princess Peach to the Shadow Queen.
Toadette helps Mario out by giving him upgrades and cheering him on. Judging by the way she acted towards him, it is believed that Toadette has a little crush on Mario.
Grodus is the main villain of the game, and the leader of the X-Nauts. Discontented to have his power limited to the moon, Grodus hopes to take over the world. He wants to obtain the Crystal Stars and unleash the Shadow Queen. His plans begin to fail when Mario obtains the magical map first. The X-Nauts are forced to follow Mario as best as they can and hold on to the hope that they will be able to outsmart or defeat him somewhere down the road.
Lord Crump is this game's analogue to Paper Mario's Jr. Troopa in that he is a strong enemy who appears in mostly odd-numbered Chapters and in the Prologue, and though a miserable failure, is completely focused on trashing Mario and his friends.
He is heavily built, wearing a purple uniform with a white X, a purple bandanna, goggles and a red and ragged scarf. He serves, or tries to serve, his master Sir Grodus, but fails most of the time because of Mario. For some reason, he has a habit of saying "Buh" and "Huh" in rhythms, most often being "Buh! Buh! Buh huh huh!" This is likely some kind of impeded or strongly accented laughing. His catchphrase is "And with that... Pow! I'm gone!"
The X-Nauts are a vile group led by the malicious Sir Grodus and his clueless vassal Lord Crump. Most are short and fat. The basic uniform for footsoldiers is red and white with a black X across the chest with goggles that stick out under a large bandanna-like piece of cloth that hides their faces and floppy ears. They salute their superior officers by crossing their arms across their chest to form an X. The X-Nauts' plan in this game is to open the Thousand-Year Door. The X-Naut Fortress is located on the moon, yet they may or may not be aliens, as they address themselves as "The secret society of the X-Nauts", which could mean that in fact they are actually beings of the Mushroom World. However, in the official website, Punio refers to them as aliens.
As a rule, they are dim-witted and easily fooled, as well as being individually weak, but in large numbers and under the guidance of Grodus they can be very dangerous. They are very loyal to their leader and usually rush unflinchingly into battle.
There are three different ranks in the X-Naut forces:
- X-Naut Trooper: The most general and weakest X-Naut, this unranked variety does not have a special title. They are field troops and the preferred underling of Lord Crump. Being the lowest rung on the ladder, they are usually the only troops sent to the Mushroom World. When on their own, they attack by either ramming people and may use potions used to boost power (by enlarging themselves) or defense. In large groups lead by higher-rank commanders, they are capable of unleashing more complex attacks through teamwork.
- X-Naut PhDs: The scientists of the X-Nauts, they wear lab coats and blue uniforms. They are in charge of designing devices the X-Nauts use for their plans, such as the Magnus Von Grapple Robots. They also use genetic engineering to create the Yux (see below) in their laboratories. When they see intruders, they will throw beakers of chemicals at them, causing various effects.
- Elite X-Nauts: The highest-ranking X-Naut Troopers, they wear red-and-black uniforms with a white X to signify their rank. They are tasked with guarding the X-Naut Fortress and are much tougher in battle than basic X-Nauts.
Their support-and-security forces come in the form of artificially created lifeforms called Yux:
- Yux: The most basic type of Yux, they are able fire shots of energy at their enemys and create Mini-Yux, which create shields around them that block all attacks. In order to defeat a Yux, the Mini-Yux must be defeated first. Like the basic X-Naut, the basic Yux is usually the only type of Yux to go to the Mushroom World.
- Z-Yux: A larger and tougher version of the original Yux, they protect the X-Naut fortress and the area surrounding it. The Mini-Z-Yux it creates are more efficient at protecting it than than the Mini-Yux.
- X-Yux: (Pronounced "Cross-Yux") A state-of-the-art Yux designed to protect the most vital areas of the X-Naut Fortress, such as Grodus' room. It is more powerful than even the Z-Yux and can sometimes immobilize invaders. Its Mini-X-Yux is more powerful than the Mini-Z-Yux, but has the same basic function. The X-Yux can summon 2 Mini-X-Yuxs in each of its turns, while the other 2 models of Yux can only summon one mini per turn.
Sometimes called the Extraordinary Computer, TEC-XX (nicknamed TEC), is a computer created by the X-Nauts to operate and maintain their moon base and gather information. He is a self-proclaimed "perfect" computer that occupies an entire room in the lowest level of the X-Naut Fortress, and often summons Princess Peach into the main computer room to ask her questions, since as he is a perfect computer, he must know everything. Peach learns he doesn't know things like love, so TEC lets her send e-mails to Mario in return for teaching him. TEC's intelligence and use of the moon base's security systems is reminiscent to 2001: A Space Odyssey's HAL 9000.
The unusual love story between Peach and TEC begins when Peach takes a shower after being imprisoned in the X-Naut's moon base. TEC, being instructed to watch Peach's every move, is overcome with feelings for Peach that he has never experienced after watching her take a shower. He calls Princess Peach to his room and she reveals to him that he must have experienced love.
The Shadow Sirens are a group of purple, shadowy creatures (perhaps demons like the similar Shadow Queen) who worked for Grodus over the course of the game. Originally, the members of the Shadow Sirens were three sisters: Beldam, Marilyn, and Vivian. After Vivian leaves, Doopliss replaces her (see bosses). Mario and his friends fight them two times: once before Vivian leaves and once after Doopliss joins the Sirens. The Shadow Sirens have strange magical attacks and are also able to hide in their own shadows. They often disappear and reappear by traveling in such a state.
As in other Mario RPGs that had parodies of famed shows and people (the Axem Rangers were a play on the Power Rangers and the Koopa Bros. a joke on the Teenage Mutant Ninja Turtles), the Shadow Sirens may be a parody of the three weird sisters from Greek Mythology and William Shakespeare's Macbeth.
- Beldam, the leader of the Shadow Sirens and the oldest sister, is a cruel hag whose pride leads her to blame Vivian for her mistakes. Her name is a word that referenced an old witch in Greek Mythology. Coincidentally, her name is also an anagram of the word "bedlam", meaning chaos. She is the shortest and resembles an old woman with long, flat purple hair, a pointed nose, and a tall blue and white striped hat. Ruling the Sirens with an iron fist, she "punishes" her sisters when they make mistakes, or as it is often in Vivian's case, are blamed for something. In battle she relies on her magical powers more than her two sisters. Not only is she a powerful offensive fighter, but she often powers up herself and her partners as well. Examples of this are when she uses a spell to use more attacks per turn than normal and when she makes her sisters huge. Symbolised by the blue on her hat, her element of choice is ice. Many speculate that the unnamed, hooded merchant who sold Princess Peach the magical map may have been Beldam, because of her statement that she had found Peach, and also the fact that Wonky calls the merchant female, and has a similar story to Beldam.
- Marilyn is the middle sister, younger than Beldam but older than Vivian. Taller and fatter than her sisters, she is also the most powerful. Her elemental attacks, as symbolized by the yellow lines on her hat, are lightning-based. Her distinguishing features are her large belly, her blonde hair with a pudding-bowl haircut, and a yellow and white striped hat. Goombella describes her as "the strong-silent type," as she rarely speaks words aside from her grunts.
- Vivian, the youngest Shadow Siren, is of average height with a rounded belly and wears a red-and-white striped hat over her curley pink hair. Because of Beldam's constant abuse, she has developed an inferiority complex. Slightly spunky, she will usually stand up for herself in such situations, usually making Beldam angrier. Her growth into a strong person and fighter begins when she meets Mario, whose name and body were at the time stolen by Doopliss. Not knowing who he truly was, she helped him out in return for his kindness. After faltering during Mario's battle with Doopliss when she found out that she had been helping her enemy, she changed sides and took down the ghost. She uses fire-based attacks, as referenced by her partially red hat, and can also protect Mario from the environment and enemies by pulling him into the shadows.
- Doopliss replaces Vivian after she and Mario defeat him. When he is with the Sirens, he simply copies his opponents' appearances and attacks rather than steal their bodies. This allows for a much more offensive fighting style, instead to the back-stabbing trickery implemented against Mario. Not much is revealed as to how well he fits in with Beldam and Marilyn, but players can assume that he is not appreciated, as Beldam's nickname for him is "freak sheet".
While Grodus believed the Shadow Sirens to have been on his side, they were in reality using him to forward their cause: reviving the Shadow Queen. Whether Vivian knew about what was to happen to Princess Peach is never addressed, but even after leaving the Shadow Sirens she still had a certain degree of loyalty to her sisters. After the Shadow Queen's defeat, Beldam and Marilyn give up evil and become the kind, loving sisters that Vivian needed. Dooplis leaves the sisters and joins Flurrie's acting troupe.
The term "party members" refers to the characters who join Mario for the entirety of his adventure and fight beside him. In addition to a unique set of moves, party members can also help out in the field, mainly to solve puzzles or offer hints. The list below is organized by the order in which the characters join Mario.
The female, college-aged Goomba working with Professor Frankly to uncover ancient treasure, she helps Mario in a manner similar to Goombario from the original Paper Mario. High on spunk and information, she is a great help to players who are confused about where they are, who someone is, or how to defeat an enemy they are facing. When not in battle, her Tattle ability gives the player helpful information on the area they are in or the person they are standing by. Famous for lacing her facts with opinions and other humorous bits, Goombella is remembered more fondly than the good-mannered Goombario. For example, she disses Beldam's snotty attitude, complains about a comment in her bestiary about Goombas being the "underlings of underlings", and notes sarcastically that it's nice to have access to a bathroom now and then in regards to a bathroom that is always occupied. She also has clear dislike for Ms Mowz, referring to her as a floozy whenever the pair meet. At the end of the game when Mario is almost done reading Goombella's e-mail, it seems as if she had a crush on him for some time.
In the Japanese version, her name is "Kurisuchiinu" (クリスチーヌ). This name is actually a pun. It's a reference to the English name "Christine", but also references the fact that she is a "Kuribo", the character known as "Goomba" in Japan.
- Headbonk - Goombella's basic attack, in which she jumps up and hits one enemy, either on the ground or in midair. If the "A" button is hit when Goombella lands on the enemy, she will jump off the enemy and land again, doubling the damage given. Goombella will take damage if the enemy has a spike or other pointy object(s) on the top of its body.
- Tattle - as one of the most unique moves in the game, this attack neither damages opponents nor directly benefits allies. Rather, Goombella reports the health, attack, and defense of the enemy it is used on in addition to any special information that may be used to defeat it. The game keeps track of a "Tattle Log," which is a bestiary of all enemies that have been tattled. The information for an enemy that can never be faced again, such as Hooktail, can be found in the trash can in Professor Frankly's house if Tattle is not used on it during the battle. Once Tattle has been used on an enemy, it is possible to see how much HP they have left during the battle, and that enemy's HP can be seen during any future encounters, as well.
- Multibonk - is similar to the normal Headbonk. This move can hit an enemy on the ground or in midair and will result in Goombella taking damage if the enemy is spiked. What is special about this attack is that each time Goombella lands on an enemy, she can attack again with a correctly timed press of the "A" button. It is hypothetically possible to continue doing this move forever. This attack is essentially the same move that Mario uses with the "Power Bounce" badge. The move costs 3 Flower Points to use and is learned the first time Goombella is powered up.
- Rally Wink - is Goombella's attack where she winks at Mario, giving up her turn in exchange for Mario to attack again. This move uses up four Flower Points and is learned by powering Goombella up a second time.
Very similar to Kooper from the first Paper Mario, Koops is a Koopa Troopa with shell-related abilities. After joining Mario in Petalburg to avenge his father's death at the hands of Hooktail, he helps out in the field by retreating into his shell letting Mario launch him at switches or distant objects to hit them or retrieve them. New to this game is the ability to hold Koops' shell in place.
After defeating Hooktail and saving his father, Koops could have settled back down into Petalburg, but he continued to adventure with Mario until the end of his adventure.
In Japan, Koops is known as Nokotarou (ノコタロウ) which comes from the name "Nokonoko", the Japanese name for the Koopa Troopa, as well as "Tarou", a common boy's name in Japan.
- Shell Toss - This is Koops's primary technique. He tucks himself into his shell and fires himself into one ground based enemy. Being protected by his shell, he is able to withstand elements such as fire or side-based spikes that several enemies use to defend themselves. The drawback is that the attack is useless against enemies on the ceiling and in midair. It can also only hit the enemy closest to players.
- Power Shell - This attack is very similar to Shell Toss, but it uses three Flower Points and causes Koops to pummel through all ground-based enemies.
- Shell Shield - A special technique that protects Mario from enemy attacks. Learned after powering-up Koops for the first time, Koops uses four Flower Points to cover Mario in a giant Koopa Shell that takes the beating for him. Based on how well players time the action command, the Shell may partially crack when it lands on the ground. If this happens, it will break after fewer attacks than if it was lowered correctly.
- Shell Slam - A special move that uses six Flower Points and over-rides enemies' defense ratings. Other than that, it is like the Power Shell move. It becomes available after the second power-up.
A famous actress who grew bored with theater life, Madame Flurrie moved to the Boggly Woods for peace and quiet. When Mario, Goombella, Koops, and Punio ask her to help them enter the Great Tree in order to save the Punies, she gladly joins them and even fights alongside them. After the X-Nauts are evicted from the tree, Flurrie decides to help Mario for the duration of his adventure. Over the course of their journey, she realizes how much she misses the stage and puts on a play of Mario's adventure with the help of a reformed Doopliss afterwards.
Her trademark is her pricey necklace, which she is never seen without. Once quite attractive, Flurrie put on weight, but still retains a trademark "curvy" appearance. Because she is a cloud spirit, she is able to use an arsenal of wind attacks to battles. When not battling, she can send out strong gusts of wind to uncover secret objects or remove objects blocking her path. Flurrie's name in the Japanese version is Clouda (クラウダ; Kurauda).
- Body Slam - Flurrie's primary attack, this sees Flurrie squishing enemies with her "stage presence," as the game describes it. This attack can be used against an enemy regardless whether it is hiding behind another enemy, is hanging from the ceiling, or is in midair. Flurrie will receive damage if she uses this attack against an enemy using protective measures such as spikes or electricity.
- Gale Force - consumes four Flower Points, but if performed correctly may cause one, some, or all of the enemies present to be blown out of battle. This move works best against easier enemies and is the most useful when there are too many enemies to handle at once.
- Lip Lock - This special attack makes use of Flurries big lip's. She sucks some Heart Points out of an enemy and uses them to replace her own. It uses three Flower Points and will be learned after powering her up once.
- Dodgy Fog - This special technique gives Mario the dodgy status, which means that some attacks from any enemy will miss him. This is especially useful when facing a large horde of enemies or a boss. It uses up four Flower Points and is learned by powering Flurrie up a second time.
Yoshi is one of the most unique partners in the game, as his appearance is determined by how much time passes between the moment the player obtains the egg and when it hatches. Colors that the Yoshi might be are green, blue, red, orange, pink, light blue and black. Being parentless, Yoshi entrusts Mario with naming him, something that the player has full control of.
Although he is not even a year old by the end of the game, Yoshi is quite smart and spunky, escaping from Hoggle the hotdog seller in Glitzville and battling alongside Mario in the Glitz Pit. Because Mario is addressed as the Great Gonzales while fighting, Yoshi learned Mario's name incorrectly and continues to call him such for most of the game. After Mario's adventure, Yoshi returns to the Glitz Pit and makes a name for himself under the title "Great Gonzales Jr.," which reveals the deep respect he has for his adopted father. He is known as "Chibiyoshi" (a cross between "Chibi" and "Yoshi") in the Japanese version.
- Ground Pound - This is Yoshi's signature technique, in which he repeatedly stomps on an enemy's head regardless of its position. The downside of this attack is that although it can be leveled up to be more powerful than the average partner attack, it is useless when facing an enemy with any defense at all.
- Gulp - A special move that uses four Flower Points. Yoshi eats the closest ground enemy and spits it back out into the enemy behind it. It is a very useful move that works against even spiked enemies and is the only way to defeat Iron Clefts.
- Mini-Egg - This special attack sees Yoshi lay a number of magical eggs that he then throws at enemies. If successful, the affected enemies will shrink, reducing their attack power. It costs three Flower Points to use and is learned after powering-up Yoshi once.
- Stampede - This is a special attack in which Yoshi whistles, summoning a herd of green Yoshis to stampede across all enemies. The attack hits multiple times, each hit taking one Heart Point from an enemy, which means that if the enemy in question has any defense at all, the attack is useless. It is learned by powering-up Yoshi twice. The attack uses six Flower Points.
- It should be noted that all of Yoshi's attacks, while they can cause a lot of damage, consist of multiple, 1 Heart Point attacks (the only exception being his Gulp move).
Vivian is an ex-member of the Shadow Sirens who abandoned them for Mario's team. She is different because unlike her sisters, she is kind and would much rather help people with her powers than hurt them. As unlikely as the friendship may be, Mario and Vivian were able to join forces without any trouble because of the conditions they had met under. Doopliss had stolen Mario's name and body, rendering the original Mario a shadowy being. Thus, Mario witnessed the true Vivian, who was his friend rather than an enemy. She helped him fight until she realized who he truly was, but returned to his side in time to save him from Doopliss and all of Mario's ex-party members, who had been tricked into helping Doopliss. After the Shadow Sirens changed their ways, Vivian returned to a much better life than she had previously had. By the end of the game, Vivian had a crush on Mario, and nearly told him of it before he boarded the boat and the party members were saying their good-byes.
Outside of battle, Vivian is similar to Bow from the first game. She can grab Mario and pull him down into their shadows, which protects them from enemies and allows them to eavesdrop on conversations. There are also several other stranger ways the move can be used.
- Shade Fist is Vivian's primary attack, which sees her hitting enemies with a fiery punch. This punch causes enemies to become burned in addition to the damage given from the punch. The burn will take away one Heart Point per turn regardless of enemy defense. Vivian will be hurt by enemies utilizing spikes and other methods of defense if she uses this attack against them.
- Veil takes one Flower Point. Vivian drags Mario and herself into their shadows in order to evade enemy attacks. However, the turn that they return from the shadows, they cannot attack. This limits the usefulness of the attack, so it is best when used against an enemy that charges up for a very powerful attack, such as a Hyper Goomba or the Shadow Queen.
- Fiery Jinx takes six Flower Points to use and attacks all enemies with a fire spell. In addition to damaging enemies, it also burns them, meaning that their Heart Points will slowly decrease until the burn goes away. Vivian obtains this attack after the first power-up.
- Infatuate confuses all affected enemies. Vivian uses four Flower Points and some flirty moves for this attack. It is more likely to work against minor enemies.
Admiral Bobbery, a salty old Bob-omb sea captain, was married to a very beautiful woman named Scarlette, and they shared many happy years together. She eventually became ill and died while he was at sea. He blamed himself for her death, feeling if he hadn't been on the voyage at sea he would have been able to make sure that she survived and so he couldn't forgive himself. Because of this Bobbery found himself unable to set sail any longer because it reminded him of his painful memories of sorrow and guilt. Close to the end of her life, Scarlette predicted that her death would bring about this pain, and so she wrote her husband a letter revealing her death wish that he continue his life as a sailor and entrusted the letter to Podley, the owner of the local cola bar. However, Podley could not bring himself to deliver the letter and held onto it for many years. Such behavior may seem strange, but this was the same Podley who abandoned his young love, Eve of Twilight Town, and later in life pretended to have forgotten her. Eventually, when Mario needed Bobbery's talent to navigate the way to Keelhaul Key, Podley had Mario to deliver the letter. Bobbery joined Flavio and Mario's journey to the Key. After they were attacked by pirate ghosts and marooned on the island, Bobbery joined Mario as a party member, and remained with him to the end of Mario's journey. In English, "Bobbery" is an outdated word that means "a loud disturbance". His Japanese name is Barel (bareru).
In the field, he uses the same attack that Bombette had in the last game: exploding to make holes in walls that are cracked.
- Bomb is Bobbery's main attack, where he walks up to the closest ground-based enemy and blows himself up. This does not hurt him and he returns to Mario's side shortly after.
- Bomb Squad sees the Bob-omb throwing several smaller versions of himself at enemies. Depending on where they land, they will damage certain enemies differently. It costs three Flower Points.
- Hold Fast costs four Flower Points to use and is learned by powering-up Bobbery once. Any enemy that directly attacks Bobbery will take damage.
- Bob-ombast is Bobbery's most powerful move. It is also the most costly, taking nine Flower Points and is learned only after powering him up twice. Bobbery lets loose an enormous explosion, severely damaging all enemies in the battle.
Ms. Mowz is an incredible sneak thief who specializes in stealing badges. As a Squeek, she possesses a very keen sense of smell. She uses this to sniff out possible items that she can take. When she wishes to blend into normal society, Ms. Mowz removes her mask and lives as the manager of the Howz of Badges at Rogueport, which is also where she sells her stolen goods. When she met Mario in Hooktail Castle, she was immediately smitten by him, much to the dismay of Goombella. Being brash and bold, she made her intentions known before leaving the fortress. Whether or not she follows Mario or if their paths simply happen to intersect by chance is unknown, but after meeting him two more times, Ms. Mowz decided to put Mario to a test. By posting a notice at Rougeport's trouble center, Ms. Mowz recruited Mario to find a badge she had cleverly hidden. After returning it to her, she decided to join Mario for the duration of the journey, hoping to find a good share of treasure by following him.
Her field ability is very useful, but not vital. She can sniff out any coins, hearts, flowers, items, key items, badges, or star pieces in the area through a sort of hotter-colder game. Although she never says exactly where something is, she will tell players if there is something of use nearby and then jump in the air when Mario is standing extremely close to the item. Players then need to find the item, which may be under an underground panel, in an invisible block, in some bushes, in a tree or similar object, or covered by part of the scenery.
Her Japanese name is Chuchuriina, which is based on "chuchu", a Japanese onomatopoeia for a mouse's squeak.
- Love Slap is the only ability in the game that breaks through enemy defenses without using up Flower Points. However, the attack power of this move is much less than the attacks of Mario's other partners, regardless of whether the enemy has defense or not. Because of this, players may only want to use Ms. Mowz against enemies with defense. Because the first two of the three slaps do no damage, Mario's audience is less entertained by this move.
- Kiss Thief is Ms. Mowz's famous move. Distracting an enemy with a kiss, Ms. Mowz can steal its item. The move costs 2 Flower Points, and causes several audience members to leave the theater. If Mario's inventory is already full, the move will automatically miss.
- Tease costs 3 Flower Points to use and confuses enemies if it is successful. Ms. Mowz produces fake copies of herself and teases enemies with a dance. It is obtained by powering-up Ms. Mowz once.
- Smooch is like converting Flower Points into Mario's Heart Points. By using 10 Flower Points, Ms. Mowz gives Mario a kiss that will heal 10 of his Heart Points. This move is gained by upgrading Ms. Mowz a second time.
These characters (excluding Luigi, Merlee, Merlon, and Merluvlee) are involved with significant points in the plotline, but usually have minor roles. Also mentioned is what chapter(s) he or she is most involved in.
- Prologue; Chapters 1, 4, and 5
Four Demons are locked in Black Chests, and beg for you to free them, saying they will help you. But when they come out, the Black Chest Demons place a curse on you. Fortunately for you, their curse is in your favor (a concept reused from several Legend of Zelda games) - they are how you obtain your four special Paper abilities (Plane Mode, Paper Thin Mode, Tube Mode, and Boat Mode). The spirits seem completely oblivious to the fact that the curses are actually helpful, but later the truth is revealed. The Black Chests are actually the Four Heroes that were involved in the sealing away of the Shadow Queen. Being cursed themselves, they had to cause a curse to whomever opened them. The heroes could never truly do this and instead offered good "curses."
Merlon is a Shaman who has the ability to raise each secondary character one level, for three Shine Sprites. It is unknown as to whether or not he is the same Merlon from Toad Town in Paper Mario, although Wonky speaks of certain occupations in which you must change your name according to what you do.
Merlee, for a fee, will cast a spell on you, and appears in battles to help you, by raising your attack or defense, raising Star Points gained, raising coins earned, raising Flower Points or Heart Points earned, or lowering Flower Point use. She always talks in rhyme.
Merluvee is a fortune teller, able to tell you where there are Star Pieces, Shine Sprites and even tell you where to go next - for a fee, of course. She once suffered a severe case of indigestion caused by a wild binge on eight Shroom Steaks.
An old man full of knowledge, he lives below Rogueport. You must pay 5 coins to gain a fact from him. He has information about recipes, hidden doors, and town gossip.
'Wonky' is an Olde English word meaning strange.
The Star-Piece collector. He'll trade you badges for Star Pieces. He will also sell Rare badges.
- Chapter 1
The mayor of Petalburg. When Mario comes and talks to him about slaying the dragon, Hooktail, Kroop gladly accepts the offer (the dragon occasionally swoops down and devours random passersby). He appears to have a hearing problem, as when Mario said his name, Kroop thought he said "Murphy" and calls him this for the rest of the game.
- Chapter 1
Koopley is Koops's dad. He went to defeat Hooktail, the dragon boss of the first chapter, but he failed. Koops decided to join Mario in defeating the dragon to avenge his father. However, when the dragon is slain, it is revealed that even though Koopley was indeed eaten up by the dragon, he hid in his shell where he was safe until Koops and Mario came and slew the dragon. In return Koopley gave Mario the Crystal Star he found in Hooktail's belly.
- Chapter 1
Koopie Koo ("Nokorin" in Japan) is Koops' girlfriend. While she started out worried something might happen to her boyfriend, Koops returns without a scratch. After that, Koopie Koo stays in Petalburg, awaiting Koops' return.
Every once in a while, he is sitting in the audience, and will occasionally assist you. He goes on adventures all during the plot. Each Chapter, he will have a new story and a new ally and eventually, you can buy a novel about him, titled 'Super Luigi', which quite obviously exaggerates the events of the quest. There are 5 volumes of 'Super Luigi' in total and the price progressively doubles.
Luigi's tales during Paper Mario 2 explain his journeys through the Waffle Kingdom as he fights to rescue the Princess Eclair.
- Chapter 2
A young Puni that you find in Rogueport Sewers, Punio helps you get to the Great Tree. He often helps you get around, and is constantly yelled at by the Puni Elder. He gets along with one certain Jabbi that can be found in the The Great Tree shop.
- Chapter 2
An elderly female Puni with a short temper. When someone calls her old, she grows to a frighteningly large size and scares the daylights out of people. Mario first meets her in a jail cell in the Great Tree soon before freeing her. In her trouble, she requests a Life Shroom due to her old age. She mispronounces Mario's name, in which she says "Marty-O".
- Chapter 2
Punio's little sister Petuni was captured by the X-Nauts along with most of the others. She is the only female Puni (besides the much older Elder). As a result, she receives a lot of attention from most Punies and even some Jabbies. She asks you every once in a while to play the "Stump Petuni" game. If you let her win by asking a certain question, she will give you a Mystic Egg.
- Chapter 3
After Mario accidentally breaks her contact lens, this spunky old Toad chef blocks his route to West Rogueport until he buys her a new one. After getting the first Crystal Star and buying a new lens for her for 10 coins, Zess T. will cook food for players when given items. After solving her trouble at the Trouble Center (giving her a cook book from the secret room in Creepy Steeple), she gains the ability to cook using two items, making a total of 57 recipes she can make.
Zess T. is likely Tayce T.'s sister. One of Wonky's stories talks of Zess T. having a sister who lives far away. However, Zess T. is much different from her sister, as seen by her unforgiving nature even after you replace her contact lense. "Stompy" is only one of the insulting nicknames she calls Mario.
- Chapter 3
Lahla is a Boo who works at Pianta's Parlor in addition to her work as a model. After convincing Mario to play the games at the Parlor by telling him she will talk about herself if he beats the high scores, she is forced to do so, revealing that she likes Honey Shrooms, is eighteen years old, is sisters with Peeka, the Boo who runs Westside Goods, and is on a diet. The influence from Bow in the last game is obvious. They are almost identical except for Lahla's lighter green color and cat ear headband.
- Chapters 3 and 6
The leader of the Pianta Syndicate, like a Pianta mafia that keeps people in line in Rogueport, Don Pianta's daughter, Francesca, ran off with one of his minions, Frankie. He wants Mario to find them and bring them back to him in return for a Blimp Ticket to Glitzville. Mario also brings back Francesca and Frankie when Don Pianta feels lonesome, and he gives him a Train Ticket to the Excess Express in return. He speaks with an Italian-American accent.
- Chapter 3
Jolene ("Kinoshikowa" in Japan) is a female Toad that works at the Glitz Pit. She seems to be up to no good, as many contestants have been disappearing, but it is revealed that she has been trying to help you in order to save her brother, Prince Mush (the first champion of the Glitz Pit). It is also implied that she is the 'mysterious lady' in the Juice Shop outside the Glitz Pit.
- Chapter 3
The big, burly champion of the Glitz Pit, Rawk Hawk ("Gold Hawk" in Japan) is undefeated. The player may at first believe he is the chapter boss but during Mario's time in the major league it is revealed Hawk's crystal star is made of glass. He is a shady character that will do anything to win when Mario, or rather, the "Great Gonzales", climbs the ranks. He resorts to attempting to poison Mario with a slice of cake, and having security lock Mario in an unused locker room prior to Mario's fight with him. However, after his defeat, he promises to fight fairly. He also appears in a humorous cutscene in the game when Bowser and Kammy Koopa arrive at his private gym. Bowser and Kammy Koopa see a "Crystal Star" on Rawk Hawk's belt hanging on the wall. When Rawk Hawk attempts to kick Bowser, Bowser simply jumps over him and squashes him. The "Crystal Star" breaks. When Bowser yells out asking what happened to the real Crystal Star and where it is, Rawk Hawk mentions that "Gonzales" took it. The name "Rawk Hawk" may be a reference to Dwayne Johnson, better known by his stage name "The Rock". At one point in the Japanese version, he declares, in English "Ai amu nanbaa wan!!" (I am number one!) "Ai amu chanpion!!" (I am [the] champion!), although in the English version, he says "Number one, baby! Rock Hawk is the Champ!". Also in the English version, his catchphrase is "Feel the Rawk!!".
- Chapters 4, 5, 6, 7, and 8
Grifty is a mysterious minstrel that hangs out on a roof in Rogueport. Over the course of the game, you can pay him 5 coins to have him recite bits and pieces of the Legend of the Four Heroes. This tale helps to explain the roots of the 1000 year-old evil that destroyed the area currently known as Rogueport, as well as some other minor bits regarding other characters, like Cortez, the pirate king, and the Great Tree's origin.
After paying the fee, the player is free to listen to his stories again anytime they wish.
Traveling Sisters 3
Three Toad sisters who are most beautiful twins. There first seen in Petalsburg in chapter one. The very first time they where seen was in Paper Mario.
- Chapter 5
Flavio is a rich, foppish merchant that, for the first four chapters, sits in Podley's Place, admiring his precious Skull Gem (which was actually stolen from Cortez by Flavio's ancestors). In chapter five, he assists you in getting to Keelhaul Key. He's not a very dependable man, and would only go with you into the jungle under pressure from the other shipmates. While he may be the "leader" figure of the crew, he is disliked by them, particularly the rough Bob-Omb pirate, Pa-Patch, who often teases him. Flavio has a tendency to speak in 3rd-person as well. His name is a reference to both his appearance and cowardly nature, as flavius means "yellow" in Latin.
The S.S. Flavion is Flavio's ship and the favourite of his fleet. The ship has a green, blue, and gold exterior; three masts (the center one having a blue and gold crow's nest); and a room for Flavio. Mario sails on the ship to Keelhaul Key, joined by Flavio, the younger brother from the Toad Bros. Bazaar (who sets up 'Keelhaul Galleria'), Pa-patch, Four-eyes (Lord Crump in a rather unconvincing disguise), Admiral Bobbery, a bunch of Bob-omb sailors, and a host of Toad sailors. The ship sails for about a week until the boat stops (while Flavio is telling a story). Ghosts attack and the ship is demolished. The incident renders Flavio the second richest man in Rogueport.
Toodles is a rich Toad who lives in Poshley Heights. While she's on the Excess Express, Doopliss steals her gold ring. After Doopliss escapes, Mario returns her ring.
A businessman, and one of the passengers on the Excess Express, he is the client of a mystery where he lost his contract for Nitro Honey Syrup. By itself, it is an excellent syrup, with powerful curative properties (Strong enough to raise the dead, it is claimed at one point). If combined with calcium and gold, however, it becomes unstable, causing a huge explosion. When Mario captures Doopliss (who had disguised himself as the famous actor Zip Toad), he recovers his contract. He is also the client of a "trouble" where he forgot the code to open his briefcase. If you tell him the code, he will reward you with some Hot Sauce.
Flavio's Bob-omb rival. After Lord Crump betrays the S.S. Flavion crew, Pa-Patch stays at Keelhaul Key for the rest of the game. He earns his name from the eye-patch he wears.
Heff T. is an overweight Toad who lives on the Excess Express. The first mystery of the chapter is when Chef Shimi's stew is stolen, and the culprit is revealed to be Heff T. When Mario uses the train to get back to Poshley Heights, he finds that Heff T. is the only passenger from the original ride. The overweight Toad explains that he's eaten so much, he can't get off the train. Because of this, he now gets his food via room service.
The spirit of a Toad who died on the Excess Express years ago, found in the passenger room next to Mario's by hiding in the room with Vivian. He steals the conductor's blanket, and will only return it if you deliver him his old diary. Mario has to recover the diary from the baggage car and bring it to Ghost T. If you read the diary, then Ghost T. will appear, scold you for invading his privacy and give you a Game Over. If you give him the diary, then he'll try to go up to "the next world", but will decide otherwise, in favor of staying on the train for a while longer, saying it had grown on him. By hiding again with Vivian after the end of Chapter 6, he will reappear, and will remain visible in the room for the remainder of the game. He later e-mails Mario, but explains that he did it by possessing the conductor.
A white Bob-omb who has been described as a wanderer. General White is first spotted in Petalburg, but wanders around the overworld. Eventually, he heads back home to Fahr Outpost, but he must be woken up with a few dozen jumps. He also works a large cannon which blasts Mario to the X-Naut base on the moon.
Goldbob is a wealthy, golden Bob-omb who lives in Poshley Heights. He owns a large and famous business called Goldbobbingtons. He is also good friends with General White. Despite living in Poshley Heights, Goldbob and his family are first spotted in Chapter 3 outside the Glitz Pit.
The wife of Goldbob. As her name implies, Sylvia is a silver Bob-omb. Unlike Goldbob, she tries her best not to spoil their son, Bub.
A bronze, spoiled Bob-omb who lives with his mother and father in Poshley Heights. When Mario boards the Excess Express, he discovers that it's little Bub's birthday, and his parents are arguing over what to get him. Neither of them knew that Bub wanted the autograph of his favourite person: the engineer.
A Bumpty (a type of penguin) who works as a museum curator, but also fancies himself a detective. When various mysteries happen aboard the Excess Express, Pennington hires Mario as his deputy to get to the bottom of them. However, he is an atrociously bad detective: he guesses nothing correctly, not even the name of his deputy (whom he repeatedly calls Luigi). He keeps the sixth Crystal Star in his museum, along with a badge that, appropriately enough, changes Mario's color scheme to match the real Luigi's.
These are the major foes in Mario's path, usually guarding a Crystal Star at the end of a chapter.
Hooktail the Dragon
The holder (or rather, the swallower) of the Diamond Star is the dragon Hooktail, found in the tower of Hooktail Castle. Hooktail attacks with fiery breath, biting attacks, and stomping moves. She has no problem with eating the Toads in the audience and does so when she is low on health (although they are released as Mario defeats her). When she is low on health, she will also attempt to trick Mario by offering to pay him 1000 coins, giving him a super-rare badge and lastly allowing him to smell the soles of her feet, something that people apparently pay much money for.
She claims to have gotten food poisoning from eating crickets once, so she becomes ill upon hearing the sound of crickets. Mario can use this to his advantage by using the Attack FX R Badge that makes his attacks sound like cricket chirps. This badge is found in a dungeon of the castle. Mario must first use his newfound "curse" to turn paper thin and walk between the bars of the dungeon cell to retrieve the badge. When he attacks while wearing this badge, Hooktail's attack is decreased from 5 to 2, and her defense is decreased from 1 to 0, making a boss that is virtually invulnerable and nearly impossible to survive at this point in the game a manageable opponent.
Hooktail has two siblings named Gloomtail and Bonetail, who live in the Palace of Shadow and in the Pit of 100 Trials, respectively. Hooktail, Gloomtail, and Bonetail were the Shadow Queen's pets before she was imprisoned the first time.
Lord Crump steals the Emerald Star in the Great Tree. After he sets off the countdown to the detonation of a bomb, Mario, his teammates and the Punies catches up to him, and Lord Crump fights Mario and his team whilst inside his newest invention, the Magnus Von Grapple, which can stomp Mario or his partner, shoot his fists out, causing them to be able to attack Mario, and can stomp the ground, creating an earthquake. Upon defeat, Lord Crump drops the Crystal Star and he and the X-Nauts are driven out of the tree.
The proprietor of the Glitz Pit, and a former arena fighter (who was considered mediocre until he found the Gold Star), Grubba uses an evil power-sucking machine powered by the Gold Star to drain the life from fighters to keep himself ultra-buff. He's a large orange creature that resembles a larger form of Tubba Blubba from Paper Mario. He primarily punches or jumps on his enemies, but can also increase his attack and defense, make himself dodgy, or attack twice each round. The disappearances of Bandy Andy, King K., and Prince Mush were all his doing; they were fighters who discovered what he was up to. He announced his intentions to drain Mario, aware that Mario was getting close to realizing what was going on.
Initially nameless (identified as "?????"), this Duplighost (ghosts that can mimic the appearance of their enemies) can also change other people's appearances, which is unique to Doopliss. He lives at the top of Creepy Steeple, just outside the village of Twilight Town. Being a prankster, he turned the residents of Twilight Towners into pigs one by one each time the tower bell chimed. After Mario defeated him for the first time, he switched bodies with Mario just as he was defeated, in effect stealing the star back before Mario ever really took it. Players then control the silhouette left in place of Mario's body. Doopliss later mocks Mario, bragging that he stole your name and body and had plans for ruining them both. Similar to the story Rumpelstiltskin, the only way for Mario to break the spell is to guess his name. Until then, he is invincible. Players who know his name beforehand will be met with a roadblock, as there is no lower-case "p" on the screen where you enter his name. The "p" must be stolen from Creepy Steeple, where his pet parrot accidentally tells Mario Doopliss's name. After Mario reveals his name, Doopliss retreats to Creepy Steeple, where he rallies Goombella, Koops, Flurrie, and Yoshi against you, tricking them into believing that he is Mario. Despite Doopliss' odd behavior (he wants to stop the quest, he hunches over, his eyes are hollow and he talks a lot for the almost mute Mario, and even addresses them as "my loyal ones".), the player's "former" party members battle Mario. After Doopliss is defeated for a second time, Mario takes his body and name back, and Doopliss escapes, humiliated. Between this and when Mario next sees him in Poshley Heights, Doopliss joins the Shadow Sirens. In the Palace of Shadow, Mario and friends fight him, along with the rest of the Shadow Sirens. At the very end of the adventure, Doopliss ends his evil ways and starts a career as an actor alongside Flurrie. His Japanese name is "Ranperu", most likely a nod to the aforementioned Rumpelstiltskin.
Cortez the Pirate King
The 1000-year-old spirit of a feared pirate king, Cortez amassed a huge treasure somewhere in Keelhaul Key, one of them being the 5th Crystal Star. It is revealed that one of the four heroes who fought the Shadow Queen 1000 years ago, a strong Koopa, had taken his star but fell from exhaustion and was so tired that he could not resist when Cortez came and pirated him, and therefore imprisoning him in the black chest. He usually appears as a huge skull, but can assume three forms. In his first, he attacks using his weapons (a hook, a rapier, a sabre, and a sword). In his second, he attacks without his weapons and occasionally charges up. In his third and deadliest form, he is able to command the weapons to attack individually, and can also bite with his skull or consume the souls of the audience to heal himself. You fight him inside his ancient pirate ship "The Black Skull", but becomes your friend after he finds out that you're only after the Sapphire Star and not his treasure. He ferries you to Keelhaul Key after Chapter 5, and allows you to use his ship to fight Lord Crump's battleship. He really turns out to be a nice giant pile of evil bones after all. He is very similar to the Tales of Symphonia side-boss skull dancer in appearance and weaponry. Cortez also occasionally speaks very limited Spanish, often calling Mario and other allies "amigo" and saying "Muy Bueno" (very good). His name is a reference to Hernando Cortez, a Spanish conquistador.
The Smorgs do not hold a Crystal Star, but they attack the Excess Express during its journey to Poshley Heights, where the sixth Crystal Star is held. The Smorg Miasma is a huge monster made up of hundreds of smaller Smorgs in the form a blob shape with either three tentacles (able to attack Mario or his partner three times in all per round) or one pincer-like protrusion (able to perform a more devastating attack on both Mario and his partner). An individual Smorg can be described as a small beast made of five black "discs" and two yellow eyes. They are first seen at the Riverside Station, where they try to prevent Mario and his teammates from lowering the drawbidge to continue the trek to Poshley Heights. Later on, the Smorgs stow away onto the Excess Express and hold all of the passengers hostage within the miasma, with the exception of the conductor. Mario and his comrades fight the entire tribe on the rooftop of the train. The miasma soon releases the petrified passengers and the Smorgs flee from the train. Due to their resemblance to fuzzy X's, they may have been designed by the X-Nauts. The nature in which they attack the train can be compared to the opening sequence of Resident Evil 0 for the GameCube.
Lord Crump is assigned to guard the Crystal Star in the X-Naut Fortress located on the Moon. He uses an upgraded version of the Magnus Von Grapple, with new attacks (a flying drill attack instead of an earth quake, and an ability to shoot many audience members at the person in front) and a higher HP amount. After defeat, the robot explodes, shooting Lord Crump into space.
By this point in the game, the player has probably been listening to Gifty's tales about the mystical history of Rogueport. There it was revealed that Hooktail was the pet of the demon that destroyed the old town, but it was also revealed that the demon had more than one pet dragon. Gloomtail is the second strongest (and second oldest) of the dragons. He looks and behaves mostly like Hooktail, except he is much stronger, and is armed with poisonous breath. In keeping with the subtle parodies of Final Fantasy series of video games, it's likely that Gloomtail is a nod to Bahamut; he is pitch black in colour, and boasts about his power, but the primary connection is his special attack, the 'Megabreath'. In the Tattle Log, it states "Watch out for his famous megabreath attack!", and Goombella says "the word is, it's GNARLY!". This appears to be a reference to Bahamut's famous 'Mega Flare' attack. It's possible that Hooktail and Bonetail, Gloomtail's sister and brother respectively, are therefore parodies of Red Dragons and Zombie Dragons, regular foes in the Final Fantasy series.
- Appearance — The Shadow Queen is the demon of the legends who destroyed the town now buried under Rogueport in Paper Mario: The Thousand-Year Door. She's a tall, purple, woman-like figure with long hair and a crown. She appears to be the queen of the mysterious shadow folk that Beldam and the Shadow Sirens belong to, resembling them greatly, except wearing a pointed gold tiara instead of a witch's hat. In fact, it was Beldam working behind the scenes that leads to her rebirth at the end of the game. Presumably she once had a body, but it is unknown what she originally looked like. When freed, she possesses the body of Princess Peach. Now, she appears to be some manifestation of dark matter or magic. She harnesses the power of the shadows to fight. Her hands can take on alternate forms, including a large group of Dead Hands reaching out of the ground to drag you into the darkness. She can absorb health from Mario and his partners, unleash status effects and use some immensely powerful attacks. Not only that, but she appears at first to be completely invincible until she is weakened by her host's last wish for peace.
- History of the Shadow Queen — In the past, she created the Crystal Stars to increase her already formidible power. She ruled one-quarter of the old city, in a palace supposedly filled with stolen treasures. She had, and still has, three pet dragons, Hooktail, Gloomtail, and Bonetail, and apparently created the infamous Pit of 100 Trials as a dungeon for those who defied her. The four heroes of legend damaged her with the Crystal Stars they stole from her, then used them to seal her deep in the Palace of Shadow, behind the Thousand-Year Door. However, before the seal was complete, she cursed the four heroes, resulting in each of them being trapped in Black Chests when they let go of the stars they all held (therefore meaning it is presumably the souls of the heroes who 'curse' Mario with his useful paper-related abilities). They made a map to the stars before they separated. Many years passed, and a new town, Rogueport, was built above the destroyed underground city, with nobody realizing that the Shadow Queen slept in the ruins below.
- The Shadow Queen's Rebirth — In the present day, Sir Grodus of the X-Nauts kidnapped Princess Peach, believing her to have the map. However, she had already passed it on to Mario. In failing to locate all but one of the Crystal Stars, he and the Shadow Sirens tricked Mario (who now possessed all the Crystal Stars upon the defeat of Lord Crump) into opening the Thousand-Year Door. When Mario and his friends caught up with Grodus, they were too late. The evil villain awakened the Shadow Queen from her deep sleep, offering her Peach's body to inhabit. But when he ordered her to attack Mario, she destroyed Grodus instead (although it seems he survived, albeit remaining a bodyless hopping head). She stated that no one controls her, and at this point Beldam, Marilyn, and Doopliss arrive on the scene. Beldam took full credit for the Shadow Queen's revival, having tricked Grodus into thinking the Shadow Queen would obey him.
- The Final Battle — The Shadow Queen asks Mario to be her eternal slave, leading to a game over if you choose to accept. Mario doesn't, obviously, and the evil witch attacks, still possessing Peach's body. She finds Peach's body too unfamiliar, so she transforms into her true form, thereby becoming invincible. Before she could destroy Mario and his friends, the Crystal Stars scattered to where they were found, and the people in each place sent their positive thoughts and wishes, momentarily disorientating the Shadow Queen and awakening Peach. Peach was able to break free from the Shadow Queen's spell long enough to give Mario her last energy, restoring his and his teammates' stats completely. Peach then appeared to fade away, giving the Queen full control. However, Peach had done what she needed, and the Shadow Queen was now vulernable. After a long duel she was defeated, and vanished forever, leaving Peach unharmed. Presumably the Shadow Queen is now defeated for good, but some presume that she was again sealed away inside the box, although the game stated that she had been "banished to the depths of the Netherworld." After her defeat, Beldam and Marilyn vanish in the shadows, leaving Doopliss to once again flee of his own accord. It is later known that the Sirens have taken a turn for the good, no longer having a reason to be evil. This implies that the Shadow Queen really is gone for good, and also that Beldam was simply doing her duty and she doesn't necessarily want the world consumed by darkness. Beldam's deeper motives and the genesis of the shadow folk is never fully revealed.
Taking the place of Culex and The Master in previous Mario RPG games, Bonetail is a final, optional challenge for masters of the game. Bonetail is the oldest of the three dragons. With 200 HP and the ability to heal himself at will, he provides the player with one last foe to conquer even after the game is finished. His attacks are the same as his brother and sister, except most will have a status effect on Mario, such as Freezing or Poison. Once you defeat him, you will receive a Badge called the Return Postage Badge. Contrary to his younger siblings, both who appear to be mindless killing machines but are actually intellectual speakers, Bonetail speaks with the exclamation "Arooo!" and variations of it, possibly because he is so ancient and just a skeleton, having not been fed for so long. On the other hand, one NPC says his name was Bonetail when he was a pet to the Shadow Queen so it is unknown if he was a skeleton back then as well.