

The last surviving Aero leaves to inform Smithy of Bowyer's death and what Geno said. Geno explains that the giant sword broke Star Road into seven Star Pieces, and asks Mario to help him find all seven Star Pieces and fix Star Road so wishes can be granted again. Together, the three of them defeat Bowyer. Mario and Mallow race into the battle and Mario saves Geno from being shot by an arrow. An Aero, one of his minions, brings him the second Star Piece. They follow him to an area where another of Smithy's minions, Bowyer, is shooting the arrows at Rose Town. Mario hears Gaz talk about it, so he and Mallow go into the forest after him.

That night, a mysterious star possesses the Geno doll and walks into the Forest Maze. Gaz accidentally knocks Mario out while playing with him. When they enter the inn, they meet a Toad kid named Gaz who plays with dolls of Mario, Peach, Bowser, and a new character named Geno. Mario gets to Rose Town to see people being hit with arrows, paralyzing them. Mario and Mallow go to Rose Town through Rose Way, at which point they see Bowser and his minions setting out to take his castle by Smithy (and he does not notice Mario, as Mario is hiding). Frogfucius also tells Mallow that he is not really a frog, and he found him in a basket one day, and tells him to go with Mario and find his real parents. The sword works for a diabolical villain named Smithy who wants to take over the world. They meet Frogfucius, who tells them that Peach is no longer at Bowser's Keep, and that the sword sent not only Mario, but Peach and Bowser flying as well. It does, and sends them down Midas River into Tadpole Pond. They travel through Kero Sewers and encounter the dreaded monster, Belome, who tries to eat them, but they defeat him and he teleports away, saying that the sewer will flood. Mallow tells Mario that his grandfather, Frogfucius, knows everything, and that he will be able to say what the Star Piece is. Mario also finds a mysterious Star Piece. With Mack gone, all the surviving Shysters run off, and Mushroom Kingdom is restored to normal. Mario and Mallow confront their boss, a dagger monster named Mack, and defeat him. Upon their return to the Mushroom Kingdom, Mario and Mallow see that it is overrun by monsters called Shysters. They defeat him, and he hands over the Frog Coin and runs off. Mario and Mallow team up and chase Croco down Bandit's Way, until they catch him and fight him. On his way out of Peach's Castle he sees that a thief named Croco stole a Frog Coin from a frog named Mallow (who doesn't even look like a frog). He enters the Mushroom Kingdom and tells the Chancellor that Bowser kidnapped Peach. Mario defeats him and his brother in battle, and when they are destroyed he takes the Hammer Bro's hammer. They head toward Mushroom Kingdom to tell the Chancellor what happened, but run into a Hammer Bro. He lands at his house, and tells a Toad who is there about this. Just when Mario is about to rescue Peach, a giant sword falls from the sky, shattering a road shaped like a star (directly above the castle) in the process, and impales Bowser's Keep, sending Mario flying.

He fights Bowser on a chandelier and defeats him, sending him falling. Bowser kidnaps Princess Peach (referred to only by her last name, Toadstool, in this game).
