|Location(s)||Peach's Castle/Toad Town Mall|
Once Bowser reaches the northern end of the beach, he encounters the Sea Pipe Statue. Because it is not in his image, Bowser attempts to destroy it, but quickly discovers that Fawful animated the statue so it can defend itself, and the statue attacks Bowser. However, after defeating it, Bowser becomes thirsty and begins to drink the water flowing out of it, allowing the Mario brothers to travel through the Pump Works. In there, the brothers recover the Stingler, the key to access the Flame Pipe. After the bros. discover and defeat Scutlet, who is blocking the pipe, Bowser regains his ability to breathe fire. Using this skill, he defeats Broque Monsieur's dog, Broggy, and continues on his quest. After discovering Broque Monsieur's shop in the woods, Bowser is asked to bring him fifteen Blitties. Once he does so, Broque will give Bowser Broggy, allowing him to use the Broggy Bonker attack.
Up ahead, Bowser notices a cage full of Goombas, trapped there by Fawful. Once he frees them, he can preform the attack Goomba Storm. He later runs into three more of his minions: Sergeant Guy, Corporal Paraplonk, and Private Goomp. The three tell him that they are attempting to recapture Bowser's castle by launching a Banzai Bill at it; they then inform him that they have the launcher, but no Banzai Bills. He goes out in search of one, instead finding a carrot in a Wiggler's garden that he thinks is a decent enough substitute. The Wiggler then emerges, angered that Bowser has plucked the carrot from the ground. However, Bowser does not care and asks if it has any Banzai Bills, to which the Wiggler replies that it does, but it will only give the bullet to Bowser if he eats the massive carrot. With help from Mario and Luigi, he completes the task, but the Wiggler forgets everything that happened, and fights Bowser, now mad that he ate the carrot. When Bowser emerges victorious, the Wiggler surrenders the Banzai Bill. On the way back to his minions, however, Bowser starts feeling stomach aches. The brothers discover that this is because of Durmite, running rampant inside his body, and take care of the issue.
After arriving back at the site of the launcher, Bowser, Corporal Paraplonk, Private Goomp, and Sergeant Guy launch the bullet at the castle. Midbus, however, takes notice of the Banzai Bill and flies the castle into the air. He then flies it to Dimble Woods, where it lands on Bowser. In order to revive him, the Mario bros. head to Rump Command, where they revive Bowser with an adrenaline boost. This also causes him to grow to a gigantic size. With his increased height, Bowser takes on his castle, damaging it to the point where Midbus flies it away. After the battle, Bowser decreases in size again, but Midbus fires a massive cannonball at Bowser. The Mario brothers once again help him by increasing his arm muscle, allowing him to throw the projectile back at the castle, permanently grounding the structure.
Once Bowser arrives in his castle, he sees that his minions have been enslaved, and that his military training facility has been converted into Fawful Theater. Bowser enters the theater, and, after noticing there are no more seats, a Goomba leads him to a "VIP" chair. After Fawful introduces the show, he announces that Bowser is the show's "special guest", and the chair rockets forward, throwing him on the stage when it stops. He is then forced into battle with Midbus again. Once Bowser emerges victorious, he is led by several Boos to a winner's feast. During the feast, however, Bowser eats so much that he becomes severely obese, falls through the floor, and becomes stuck; it is at this point that Mario and Luigi can access the Flab Zone.
Some time later, Fawful uses a ray gun to remove Peach from Bowser's body. After retrieving Peach, Bowser falls through the floor and onto a treadmill brought out by Midbus, and uses it to literally burn the fat he gained. However, he then walks over to a crate of Bob-ombs, still on fire, only noticing the sign telling what room he is in, and unintentionally lighting a Bob-omb. This Bob-omb leaps into a crate full of others, creating a chain reaction which blows up the other crates and sending Bowser flying into an underground tunnel. Soon after, he meets a group of Monty Moles, who he learns are building a tunnel all the way to Toad Town. With Bowser's help, the tunnel is finished, but he wanders down a path that activates a security system that knocks him unconscious.
He later regains consciousness and travels to Doctor Toadley's office, where he encounters the Mario brothers and battles them. After Mario and Luigi win, the doctor tells the trio that they need to find the three Star Cures to cure the Blorbs and find a way into the castle. He then tells them that the first cure is held by Durmite, located in Dimble Wood. Overhearing this, Bowser runs off toward the woods.Bowser is later at Bubble Lake when the brothers lose Durmite in the Energy Hold of Bowser's body. Thanks to them enhancing Bowser's sneezing, he is able to cross the river and activate a propeller mechanism. This causes the entire Tower of Yikk to fly out of the lake and onto Bowser. The Mario bros. head to Rump Command again to revive him and increase his size. After defeating the tower, it is immobilized, allowing Bowser to enter. Through a holographic image inside a book, he meets Yikk, who guides him through the use of the Boo-Ray Machine. By using this machine, Bowser is able to help the brothers get the Star Cure from Durmite, who transforms into Wisdurm, and learn the Body Slam technique, which allows him to escape the tower.
Once outside, Bowser encounters Private Goomp and the others, and asks them if they had seen a Star Cure. They reply by saying that Bowser keeps a Star Cure like object in his vault back in his castle. He journeys there, and finds that the underground path he helped dig is now Fawful's property, and that it is in use for the Fawful Express. The express prepares to leave the castle, with Bowser on the tracks, and it eventually rams him into a rock. Mario and Luigi once again go to Rump Command, revive Bowser, and increase his size. He then proceeds to destroy the train before shrinking back to normal. Once he returns to the vault, he finds the safe, but cannot remember the code to open it. The Mario brothers then journey to Bowser's Memory Banks and, after defeating the guardian, jog Bowser's memory by reassembling the memory containing the code. He opens the safe and claims the second Star Cure, but Private Goomp, Corporal Paraplunk, and Sergeant Guy, who are now under Fawful's command, shove him into the safe. Bowser then eats the Star Cure, which is found by Mario and Luigi in his gut.
Eventually, he is freed from the safe, but his back hurts after being crammed inside it for too long. Inside the Lumbar Nook, Mario and Luigi eventually loosen his back, enabling Bowser to use the Spike Ball move. He then continues his search for Fawful inside Peach's castle. However, during his search, he finds two Piranha Plants, whose fireballs force Bowser to curl into a ball. The brothers travel to the Chest Station and give impulses that allow Bowser to fly into the air. After defeating the plants, Bowser notices Fawful and Midbus using Peach to awaken the Dark Star. Fawful manages to escape, and leaves Midbus, whom he transforms into Blizzard Midbus, to defeat Bowser. However, once Blizzard Midbus is defeated, he is trapped in a block of ice, with cold air blowing out of his snout.
He then continues on to Fawful, who is absorbing power from the Dark Star. However, Bowser interrupts the process by punching him. The Dark Star then heads inside Bowser's body, the heat from the star inside him so intense that he uses Midbus' icy breath to cool his throat. This allows Mario and Luigi to travel through the Airway. After the bros. defeat the Dark Star in battle, it leaves Bowser's body and, having absorbed some of Bowser's DNA, transforms into Dark Bowser; however, since it only has a portion of its power at the moment, the transformation is incomplete. It then runs off, with Bowser in tow.Bowser chases the Dark Star until he reaches the courtyard of Peach's Castle, where Fawful activates the building. The castle transforms into a robot, and stomps Bowser. The Mario bros. head to Rump Command, revive Bowser, and make him a giant once again. Bowser faces the castle in battle, and, upon emerging victorious, heads back inside and fights Fawful, who transforms himself into Dark Fawful. Fawful's body is destroyed when he loses, but he survives as a mass of dark energy. Fawful is then absorbed by the Dark Star, which is able to complete its transformation into Dark Bowser, then escapes using a hidden passage.
After chasing Dark Bowser to a high tower above the castle, he encounters him on the opposite end, an unconscious Peach nest to him. Dark Bowser then claims that he is going to rule the world, and covers the Mushroom Kingdom in a veil of darkness, a hurricane sucking up its various inhabitants. Starlow attempts to reveal that Mario and Luigi are inside his body at this point, but Bowser cannot hear. He then engages in the final battle with Dark Bowser. During the fight, he manages to defeat Dark Bowser, but Fawful revives him and makes him giant. Bowser then knocks Fawful out of his dark half's body, and sucks him up using his vacuum ability, allowing Mario and Luigi to defeat him from the inside. After Fawful and the Dark Star Core are defeated, Bowser is able to destroy his now unstable dark counterpart, eliminating him once and for all.
However, inside Bowser's body, Fawful is still alive, and, in one final attempt to defeat Mario and Luigi, self-destructs. This does not kill them, and instead sends them and everyone else inside his body flying to the outside world once more. Bowser is confused at first, but slowly figures everything out, including the fact that Starlow was the one giving him advice the entire time, under the alias "Chippy". This greatly angers him, and, as the credits roll, he engages in battle with the Mario brothers once more, loses, and is carried back to his castle.
Back at the castle, an injured, bedridden Bowser is still overseeing reconstruction of his castle. Private Goomp, Corporal Paraplonk, and Sergeant Guy then enter the room, begging for their positions back. Birdley, Dr. Toadley's bird, then flies in and drops a box onto Bowser's bed. Starlow emerges, wanting to check on him, fearing that he may attack Peach's castle again, though Bowser tells her that he is focusing on rebuilding his own castle at the moment, then, still angry about the truth, yells at her to leave. After she does so, he yells at the trio who previously entered, telling them to work on rebuilding the castle. Once Bowser is alone, he opens the box, revealing a cake with Bowser, Mario, Luigi, Peach, and various other decorations on it.
Bowser's normal battle system is similar to Mario and Luigi's but still contains differences. One such difference is his attack options; his basic attacks are the Punch and Fire Breath. His third option is the Vacuum Block, which allows him to inhale small enemies, items, and sometimes Blitties; any enemies sucked inside him are fought by Mario and Luigi. His final attack option is his own variant of special attacks, which generally involve Koopa Troop soldiers coming to Bowser's aid. When being attacked, Bowser has two forms of defense: He can curl into his shell, or he can counterattack by punching.
During giant Bowser battles, the player must hold the DS on its side. Bowser only has two attacks: punching, achieved by swiping the stylus across the Touch Screen, and breathing fire, achieved by the player blowing into the microphone. Occasionally, Mushrooms also appear during battle, which can be used to heal him.
Bowser's ranking system is also different. It starts at Bronze Boss as the default and changes to Silver Boss at level 10, Gold Boss at level 20, and Final Boss at level 40.Additionally, in the Flab Zone, the brothers occasionally encounter Nutsoglobins, who are not mandatory, but can help in navigating the area. They ask them trivia questions about Bowser, but, before they so, they allow the player to ask Bowser questions, with the Nutsoglobin being the mediator between them; each question asked costs five coins. They then ask the player the questions, which are based upon what Bowser says in response to the possible he or she can ask him. Whenever a Nutsoglobin talks to Bowser from inside his body, Bowser does not know who it is that is speaking.
A boss called Bowser X appears in the Challenge Node in Bowser's body and can be fought by Mario and Luigi. To get to him, the player must beat all X bosses, and then face all the other X bosses in a row before facing Bowser X. He is, by far, the strongest boss in the game. He is also the only X boss without a color change from the original. While this is clearly not the real Bowser, such an entity existing inside of him may have been the result of the Emoglobin at the Gauntlet within creating it to challenge the Bros. further, after besting all of the other X bosses.
Like all the other X Bosses in the Challenge Node, Bowser X has upgraded stats and additionally, he is capable of performing all of original Bowser's attacks, plus three new ones. However, Bowser X does not use the remaining troops later on in the battle. Attacks Bowser X performs during battle include:
- Punch - A variant of Bowser's fist attack which is slightly faster than the original one. Mario and Luigi must jump to avoid taking damage. Every once in a while, his nostrils smoke out. When this happens, he completely misses the punch and jumps over the Bros. in clumsiness. Mario and Luigi should not jump during this attack.
- Flame - A fire-based combat technique. It can be avoided by grabbing onto Starlow before Bowser X launches the attack. If the player misses, the attack deals massive damage to the Bros.
- Goomba Storm - This attack has two phases. At first, Goombas run after Mario and Luigi, while Bowser X sets some of them on fire. After that the burning Goombas fall from the sky and the player must use the hammer attack to hit them back. They move at a much faster speed than the original.
- Shy Guy Squad - This attack is similar to Bowser's attack. It can be countered by a timed hammer attack.
- Fireball - Bowser X shoots a simple fireball at one of the Bros.. The attack doesn't do much damage, but he continues to execute this attack over and over. The Bros. must hammer the fireball back at Bowser to damage him. Doing this causes Bowser X to curl up into a ball and head for the upper portion of the screen. There, a rain of fireballs drops from Bowser X at random times. The Bros. must hammer the fireballs when they're above them directly. The final part of this attack is when Bowser X, still curled up, attempts to ram himself onto one of the Bros., heavily damaging him.
- Giant Bowser X - Bowser X grows in size and attacks the Bros. with a barrage of fireballs. The Bros. should jump only when the fireballs head toward the Bro. directly. The Bros. shouldn't jump when the fireball passes overhead. After Bowser X finishes that, he proceeds to chase the Bros.. They must jump over the fiery obstacles and head for the two springs waiting at the end without taking major damage.
- Vacuum - A counter move used every time when the player uses a special attack. Bowser X inhales the used move, making it inaccessible for five turns.