Princess Peach's Castle is the first place of the game. The game begins at the castle, with Mario and Luigi traveling through the main interior to the meeting room. The meeting is about the Blorbs that have infected much of the Mushroom Kindgom. The meeting is soon cancelled as Bowser comes into the meeting, angered by the fact that they don't believe he is there to solve the unknown disease. After Mario defeats him, Peach and Starlow send him out of the castle. Later on, Brainwashed Bowser enters the meeting room as everyone leaves, inhaling everyone in the room. Bowser then ends up knocking out, and Fawful appears, sending him out of the castle yet again.
It is seen later again, yet blocked off by Fawful using the Dark Star power. He has now taken over the castle, serving it as his chamber to reviving the Dark Star. Once Mario and Luigi combine the Star Cures into the Miracle Cure, they are able to bring down the barriers and enter the castle. They have to travel through Peach's Castle Garden and fight Junker before they find Bowser all sore. There is a pipe that leads to him in the gardens.
Once the Mario Bros heal Bowser, the great beast is now about to explore deep into the castle walls using his new ball roll. He finds that Fawful has made a trial for Bowser, leaving three keys to three of his hovering bots that hold the whereabouts of either treasures or the way out. After a long chase and crushing the bots, Bowser makes his way through the next area where Fawful has giant Piranha Plants growing. Once weeding the humongous plants, he moves on to the room that Fawful, Midbus, the Dark Star, and Princess Peach reside in.
Fawful allows Midbus to fight against Bowser, giving him an icy powerup to make him Blizzard Midbus. Yet Bowser proves himself the stronger beast, defeating and freezing Midbus in place. But it is too late for the main goal of rescuing the princess as the Dark Star is fully revived. Fawful is able to take some of the energy from the Dark Star before Bowser punches him out of the room. The Dark Star enters Bowser's Body, entering from the mouth while Bowser chuckled at the pleasure of punching Fawful.
Once the Mario Bros defeat the weakened Dark Star, it escapes out of Bowser's Body, in a phantasm form of Bowser (as a result of Bowser's DNA). Bowser chases the ghost out into the Castle Courtyard, where the entire castle comes to life. The massive fortress transformed into a battling machine by Fawful. Bowser must become giant for the last time in order to defeat the castle. After a deadly battle, the Castle is defeated, and Bowser shrinks back to normal size.
Heading back into the meeting room, Bowser finds Dark Fawful searching for the Dark Star, and attacks him. Once Bowser damages Fawful beyond limits, Dark Fawful transforms into a bug-like stage, crawling out of the room. Outside the room, The Dark Star and Dark Fawful merge together to become the stable Dark Bowser duo. After Dark Bowser escapes through a hidden passage behind the throne, he and Bowser engage in a spike ball battle up the central tower with Bowser being the victor. Following Dark Bowser, Bowser ends up on the final battle arena.
In the arena, Dark Bowser releases a hurricane of Dark smoke that covers the entire Mushroom Kingdom. He explains how he is going to rule over the pathetic land, and that there is nothing standing in his way. Bowser then laughs at his words, stating that this is HIS land, and that he can't win. They then begin the final Battle; Bowser versus Dark Bowser and Mario Bros versus Dark Star Core. After a long battle, the Mario Bros defeat the Dark Star Core, allowing Bowser to finally give the final blow to the now unstable Dark Bowser.
The Mushroom Kingdom returns to normal, except the fact that Fawful is still alive. After a quick speech, Fawful explodes in order to kill the Mario Bros. Yet it backfires as it sends all that were trapped in Bowser's Body out into the Mushroom Kingdom. Everyone celebrates at making it out, except for the confused Bowser, just now finding out that Mario and Luigi were in his body the entire time. After learning who Chippy was, he reached his last straw, making a final battle with the Mario Bros leading into the cutscenes in the end credits.
Enemies (including bosses)