At Peach's Castle, everyone has come to celebrate the Mushroom Maze Competition, including Bowser and his forces, who have agreed to a temporary truce. Before Peach can get the festivities started, a bolt of purple lightning strikes the castle. Mario looks for the bolt's origin and sees a dark cloud blowing straight toward the castle. The cloud engulfs the castle, leaving a deep haze. Through it, Mario can see a shadowy skeletal figure holding a dark cube, Mario jumps and swipes it from the figure who gets angry and kidnaps Princess Peach. The figure then proceeds to corrupt most of Bowser's minions before making his exit. After the haze clears, Mario looks around to see that the castle and the decorations for the competition are just destroyed. He finds Toad who wonders what happened and notices the cube in Mario's pocket. Toad recognizes it as the Shadow Cube, and says that they could use it against that figure. Mario then looks out to see some areas in the Mushroom Kingdom are shrouded in darkness. He rallies Luigi, Bowser, Donkey Kong, and Yoshi to join him in reclaiming the Mushroom Kingdom.
Upon reaching the Mushroom Fields, Mario and the others run into a Koopa Troopa, corrupted by the power of the figure, who challenges Mario to a Maze Race. Upon defeating the Koopa Troopa, Mario and Bowser demand that it tells who the figure is. Still corrupted, the Koopa Troopa refuses and flees back through the Fields. They follow in hot pursuit and meet up with a corrupted Shy Guy, who challenges the group. After being defeated, the Shy Guy lets it slip that "Lord Byrinth shall regain the Shadow Cube." before fleeing back into the plains.
Finally, at an altar at the end of the plains, Mario and the crew meet the figure who announces himself as Lord Byrinth, and that the kingdom is now his. Bowser is majorly against this and promises to pummel the Lord at the earliest opportunity. Lord Byrinth is not amused by Bowser's comment and wakens Petey Piranha who was sleeping nearby. Byrinth corrupts Petey and forces it to attack Mario and the gang. After beating Petey, Mario notices that the Shadow Cube is glowing and holds it out to the fog. Suddenly the Cube fires a blast at the fog and clears it, revealing the Sweet Sweet Desert. Bowser then says that the cube will either help us or destroy us, before running into the desert, forcing the others to follow him.
Meanwhile, on the other end of the field, Lord Byrinth is upset at Mario's skill in beating Petey Piranha. Peach, who is in a cage, objects to his point of view about Mario before he silences her. Byrinth then proceeds to try another attempt at Mario's life, before saying that he must get that cube back.
Mission: Defeat Koopa Troopa in a Maze Race!
Mission: Defeat Shy Guy in a Maze Race!
Mission: Defeat Petey Piranha!
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Mission: Block 3 Attack Items using a Defense Item!
Mission: Reach the Super Star before Koopa Troopa and Shy Guy!
Mission: Defeat Wario in a Maze Race!
Mission: Defeat Whomp in a Battle!
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Mission: Defeat Dry Bones in a Maze Race!
Mission: Use a Boo to steal an Item from your opponent!
Mission: Reach the Super Star before Koopa Troopa, Shy Guy and Mechakoopa!
Mission: Defeat King Boo in a Battle!
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Mission: Reach the Super Star before Daisy!
Mission: Defeat Wario in a Battle!
Mission: Reach the Super Star using only Assist Items!
Mission: Defeat Gooper Blooper!
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Mission: Defeat Mechakoopa in a Maze Race!
Mission: Reach the Super Star using only Defense Items!
Mission: Defeat Waluigi in a Battle!
Mission: Defeat Bowser Jr. in a Battle as Bowser!