Mario sets out to rescue Princess Toadstool, infiltrating the castle to which she has been taken and challenging kidnapper King Bowser.[2] During the battle, a giant living sword named Exor falls from the sky, breaks through the Star Road (a pathway that helps grant people's wishes), and crashes into Bowser's castle,[2] sending Mario, Princess Toadstool, and Bowser flying in different directions, as well as scattering the seven star fragments. Mario lands back at his pad and meets up with Toad, who tells him he has to rescue Toadstool. Mario returns to Bowser's castle, but Exor destroys the bridge, preventing him from entering.[5] Mario makes his way to the Mushroom Kingdom, where Mario encounters a "tadpole" named Mallow who has set out to retrieve a frog coin taken by the local thief Croco.[6] After Mario helps him retrieve the frog coin, they return to the Mushroom Kingdom to find that it is overrun by the Smithy Gang, followers of the evil robotic blacksmith king named Smithy. Mario and Mallow enter the castle to defeat gang boss Mack,[7] and subsequently find a mysterious Star Piece. Mallow accompanies Mario to Tadpole Pond so they can get advice from Frogfucious, Mallow's grandfather. He reveals that Mallow is not really a tadpole, and says Mallow should join Mario on a quest to find the seven Star Pieces as well as Mallow's real parents.
The duo travel to Rose Town where they meet a star spirit who has taken control of a silent doll named Geno. After battling the bow-like creature Bowyer, who is immobilizing residents of Rose Town with his arrows, they retrieve another Star Piece. Geno joins Mario and reveals to him the Star Piece is a part of the shattered Star Road, where he normally resides. Geno has been tasked with repairing Star Road and defeating Smithy, so that the world's wishes may again be heard.[8] The trio eventually head to Booster Tower (the home of the eccentric amusement-venue owner, Booster), where they encounter Bowser, whose minions have all bailed out on him. They join forces (calling a truce in the process) to fight a common enemy, as Bowser wishes to reclaim his castle. The new team intercepts Princess Toadstool just before she is forcibly married to Booster, but it turns out that the wedding wasn't real and that Booster only wanted the wedding cake.[9]
After her rescue, the princess returns home to Mushroom Kingdom only to then decide to join the party while her grandmother takes her place in disguise.[10] After gathering five star pieces, they search Nimbus Land. A statue maker informs them that Valentina has the rulers of Nimbus Land being held captive, and her sidekick Dodo is impersonating the prince. Dodo would make Valentina his queen. The statue maker recognizes Mallow as the true prince, then disguises Mario as a statue to infiltrate the castle. There they defeat Valentina and Dodo. The newly liberated king and queen, Mallow's parents, inform the group that they saw a star fall into the nearby volcano.
After traveling to Barrel Volcano to obtain the 6th Star Piece, Mario's party learns that the final piece must be held by Smithy in Bowser's castle.[11] They battle their way through the assembled enemies to enter the castle, where they discover that Exor is actually a gateway to Smithy's factory, the place Smithy mass-produces his army.[12] Mario and company cross over, find the heart of the factory, and defeat Smithy, thereby stopping his army creation and causing Exor to disappear. The collected Star Pieces are used to repair the Star Road, Geno returns to the Star Road, Bowser rebuilds his castle with his newly reformed army, Mallow regains his rightful title as prince of Nimbus Land, and Mario and Princess Toadstool return to the Mushroom Kingdom to celebrate their victory.[13]