The story begins with Mario entering Bowser's Castle to rescue Princess Toadstool. Mario defeats Bowser, but a giant earthquake caused by a sword named Exor shakes the castle, sending Mario, Bowser, and Princess Toadstool flying in three different directions. Mario falls through the chimney into his house and returns to the Mushroom Kingdom with Toad to inform the Chancellor of the current situation. The Chancellor insists that Mario locates the Princess, defeats Bowser once and for all, and discovers the truth behind the sword's intentions. Upon exiting the Chancellor's castle, Mario finds a new character named Mallow, who starts crying after his grandfather's coin is stolen; Mario helps Mallow retrieve the coin from Croco.
Mario and Mallow return to Mushroom Kingdom so Mallow can complete his errand, but they find the Kingdom under attack. After defeating Mack, they discover their first Star Piece, which the Chancellor suggests is connected to the arrival of Smithy. Mario and Mallow head to Tadpole Pond to see Mallow's grandfather, Frogfucius, for more information on Smithy's forces. However, Frogfucius is unable to help them and instead urges Mallow to aid Mario in his quest.
With the assistance of Geno, a star spirit who assumes the identity of a doll, Mario and Mallow manage to get the second Star Piece. Geno thanks them and introduces himself as a visitor from the Star Road. He explains how Exor shattered the Star Road into seven Star Pieces, and that all seven must be recovered to repair the Star Road. With the mystery behind the origin of the star pieces finally solved, Geno joins the party and they set out to search for the remaining five pieces and Peach.
The heroes next arrive at Moleville where a shooting star has crashed into the hollowed-out mountain on the outskirts of town and trapped two kids that had been exploring inside. The party retrieves the two missing kids and the third Star Piece. While in Moleville, Mario also sees Bowser trying to reassemble his forces.
When the crew receive word that someone was seen falling from the sky and landing on the roof of Booster Tower, the home of a rich and greedy madman, they decide to check it out. When they arrive, Bowser is seen standing outside the entrance, reminiscing about his own castle and how much he misses it. When the party explains how Smithy's involvement has affected Star Road, Bowser reluctantly decides to join up with Mario and his friends and works to stop Smithy in order to get his castle back. Bowser's help comes in handy, but Booster manages to escape with Peach and takes off for the nearby town of Marrymore in an attempt to marry her.
Upon arriving in Marrymore, the heroes learn that Booster has kicked everyone out of the chapel and barricaded the doors. Fortunately, they find the Back Door, and manage to rescue Peach after Booster gets distracted by the enormous wedding cake.
Finally, with the Princess found, the party returns to the Mushroom Kingdom and explains the situation to both her and the Chancellor. Against the wishes of the Chancellor, the Princess decides to join the party. On Frogfucius' advice, they head to Star Hill, where the party discovers the fourth Star Piece.
The quest for the three remaining Star Pieces brings the party to Seaside Town, where the elder of the town informs the party that a Star Piece has fallen into the ocean and likely is controlled by a ruthless pirate called Jonathan Jones. The party finds Jones' Sunken Ship and manages to defeat Jones, earning the party the fifth Star Piece and Jones' respect.
They return to Seaside Town and find out that the elder of the town was Yaridovich, a spear-themed member of the Smithy Gang, in disguise. In exchange for releasing the citizens of the town, Yaridovich demands the fifth Star Piece. Yaridovich's departure is delayed by Jones, which allows the party to defeat Yaridovich to regain the Star Piece.
The party's journey continues through Land's End, a desolate conglomeration of mountain and desert regions, and Monstro Town, a place teeming with reformed monsters. With some help from the town's residents the party scales an inaccessible cliff in order to get to Bean Valley, which leads to a city in the sky.
The city, Nimbus Land, is made up of inhabitants who look just like Mallow. As the party arrives, the royal adviser Valentina announces that the King's ill condition has turned critical. However, she also claims to have found the lost prince who takes over for the ill king; Valentina becomes the new queen when the prince asks her to marry him.
Looking around the city, Mallow learns from the royal sculptor that he is the real prince. Garro, a Nimbus Land citizen, is able to sneak the party into the castle in order to rescue the king and queen. Seeing the real prince, Valentina and the impostor Dodo flee. After briefly falling out of Nimbus Land, the party defeats Valentina and Dodo, making them flee to Booster's Tower. They get the key and rescue Mallow's parents, the king and queen. Both are unharmed and perfectly healthy.
After Mallow's reunion with his parents, the party continues onward, told by the queen that a star fell into the Barrel Volcano. The party finds the sixth Star Piece, but it is stolen by the Axem Rangers, an elite Smithy Gang fighting force. After chasing them onto their warship, named Blade, the party defeats the Rangers.
The last star piece is in Bowser's Keep. After battling through many of Smithy's elite forces, the party battles Exor. Defeated, Exor transports them to a dark and lifeless factory, the center of Smithy's operations.
The party makes its way through the factory and confronts Smithy. After being defeated, Smithy destroys the factory, and reveals his true form. Despite this, he is defeated and explodes.
With Smithy gone and the final Star Piece in hand, Geno thanks the party and returns to the Star Road to repair it. The party heads outside in time to see Exor disintegrate.
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